[{"department":[{"_id":"RoSe"}],"file_date_updated":"2023-12-11T12:03:12Z","ddc":["510"],"date_updated":"2023-12-11T12:12:14Z","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14662","volume":13,"issue":"3","file":[{"success":1,"file_id":"14677","checksum":"9ce96ca87d56ea9a70d2eb9a32839f8d","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_JST_Seiringer.pdf","date_created":"2023-12-11T12:03:12Z","creator":"dernst","file_size":201513,"date_updated":"2023-12-11T12:03:12Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1664-0403"],"issn":["1664-039X"]},"publication_status":"published","month":"11","intvolume":" 13","scopus_import":"1","oa_version":"None","abstract":[{"text":"We consider a class of polaron models, including the Fröhlich model, at zero total\r\nmomentum, and show that at sufficiently weak coupling there are no excited eigenvalues below\r\nthe essential spectrum.","lang":"eng"}],"title":"Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"Yes","external_id":{"arxiv":["2210.17123"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory. EMS Press, 2023. https://doi.org/10.4171/JST/469.","ista":"Seiringer R. 2023. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 13(3), 1045–1055.","mla":"Seiringer, Robert. “Absence of Excited Eigenvalues for Fröhlich Type Polaron Models at Weak Coupling.” Journal of Spectral Theory, vol. 13, no. 3, EMS Press, 2023, pp. 1045–55, doi:10.4171/JST/469.","ieee":"R. Seiringer, “Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling,” Journal of Spectral Theory, vol. 13, no. 3. EMS Press, pp. 1045–1055, 2023.","short":"R. Seiringer, Journal of Spectral Theory 13 (2023) 1045–1055.","apa":"Seiringer, R. (2023). Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. EMS Press. https://doi.org/10.4171/JST/469","ama":"Seiringer R. Absence of excited eigenvalues for Fröhlich type polaron models at weak coupling. Journal of Spectral Theory. 2023;13(3):1045-1055. doi:10.4171/JST/469"},"date_published":"2023-11-25T00:00:00Z","doi":"10.4171/JST/469","date_created":"2023-12-10T23:00:59Z","page":"1045-1055","day":"25","publication":"Journal of Spectral Theory","has_accepted_license":"1","year":"2023","publisher":"EMS Press","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"In order to demonstrate the stability of newly proposed iridium-based Ir2Cr(In,Sn) and IrRhCr(In,Sn) heusler alloys, we present ab-initio analysis of these alloys by examining various properties to prove their stability. The stability of these alloys can be inferred from different cohesive and formation energies as well as positive phonon frequencies. Their electronic structure results indicate that they are semi-metals in nature. The magnetic moments are computed using the Slater-Pauling formula and exhibit a high value, with the Cr atom contributing the most in all alloys. Mulliken’s charge analysis results show that our alloys contain a range of linkages, mainly ionic and covalent ones. The ductility and mechanical stability of these alloys are confirmed by elastic constants viz. Poisson’s ratio, Pugh’s ratio, and many different types of elastic moduli."}],"oa_version":"None","publisher":"Elsevier","quality_controlled":"1","scopus_import":"1","intvolume":" 674","month":"11","publication_status":"epub_ahead","year":"2023","publication_identifier":{"issn":["0921-4526"]},"language":[{"iso":"eng"}],"publication":"Physica B: Condensed Matter","day":"28","date_created":"2023-12-10T23:00:56Z","doi":"10.1016/j.physb.2023.415539","volume":674,"date_published":"2023-11-28T00:00:00Z","_id":"14652","article_number":"415539","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-12-12T08:22:23Z","citation":{"chicago":"Gupta, Shyam Lal, Saurabh Singh, Sumit Kumar, Unknown Anupam, Samjeet Singh Thakur, Ashish Kumar, Sanjay Panwar, and D. Diwaker. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter. Elsevier, 2023. https://doi.org/10.1016/j.physb.2023.415539.","ista":"Gupta SL, Singh S, Kumar S, Anupam U, Thakur SS, Kumar A, Panwar S, Diwaker D. 2023. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 674, 415539.","mla":"Gupta, Shyam Lal, et al. “Ab-Initio Stability of Iridium Based Newly Proposed Full and Quaternary Heusler Alloys.” Physica B: Condensed Matter, vol. 674, 415539, Elsevier, 2023, doi:10.1016/j.physb.2023.415539.","short":"S.L. Gupta, S. Singh, S. Kumar, U. Anupam, S.S. Thakur, A. Kumar, S. Panwar, D. Diwaker, Physica B: Condensed Matter 674 (2023).","ieee":"S. L. Gupta et al., “Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys,” Physica B: Condensed Matter, vol. 674. Elsevier, 2023.","ama":"Gupta SL, Singh S, Kumar S, et al. Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. 2023;674. doi:10.1016/j.physb.2023.415539","apa":"Gupta, S. L., Singh, S., Kumar, S., Anupam, U., Thakur, S. S., Kumar, A., … Diwaker, D. (2023). Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys. Physica B: Condensed Matter. Elsevier. https://doi.org/10.1016/j.physb.2023.415539"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Gupta, Shyam Lal","last_name":"Gupta","first_name":"Shyam Lal"},{"first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","full_name":"Singh, Saurabh","last_name":"Singh"},{"last_name":"Kumar","full_name":"Kumar, Sumit","first_name":"Sumit"},{"first_name":"Unknown","last_name":"Anupam","full_name":"Anupam, Unknown"},{"first_name":"Samjeet Singh","last_name":"Thakur","full_name":"Thakur, Samjeet Singh"},{"first_name":"Ashish","last_name":"Kumar","full_name":"Kumar, Ashish"},{"first_name":"Sanjay","last_name":"Panwar","full_name":"Panwar, Sanjay"},{"first_name":"D.","last_name":"Diwaker","full_name":"Diwaker, D."}],"title":"Ab-initio stability of Iridium based newly proposed full and quaternary heusler alloys","department":[{"_id":"MaIb"}]},{"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"}],"citation":{"ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840.","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.","ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107840","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","ieee":"S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Silvia","full_name":"Scarpetta, Silvia","last_name":"Scarpetta"},{"first_name":"Niccolò","full_name":"Morrisi, Niccolò","last_name":"Morrisi"},{"first_name":"Carlotta","full_name":"Mutti, Carlotta","last_name":"Mutti"},{"first_name":"Nicoletta","full_name":"Azzi, Nicoletta","last_name":"Azzi"},{"first_name":"Irene","full_name":"Trippi, Irene","last_name":"Trippi"},{"first_name":"Rosario","full_name":"Ciliento, Rosario","last_name":"Ciliento"},{"last_name":"Apicella","full_name":"Apicella, Ilenia","first_name":"Ilenia"},{"first_name":"Giovanni","full_name":"Messuti, Giovanni","last_name":"Messuti"},{"last_name":"Angiolelli","full_name":"Angiolelli, Marianna","first_name":"Marianna"},{"orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","last_name":"Lombardi","first_name":"Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"}],"external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"article_processing_charge":"Yes","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","quality_controlled":"1","publisher":"Elsevier","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"20","publication":"iScience","page":"107840","date_published":"2023-10-20T00:00:00Z","doi":"10.1016/j.isci.2023.107840","date_created":"2023-02-02T10:50:17Z","_id":"12487","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-12-13T11:11:24Z","ddc":["570"],"file_date_updated":"2023-10-09T07:23:46Z","department":[{"_id":"GaTk"}],"abstract":[{"lang":"eng","text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","month":"10","intvolume":" 26","publication_identifier":{"eissn":["2589-0042"]},"publication_status":"published","file":[{"success":1,"checksum":"f499836af172ecc9865de4bb41fa99d1","file_id":"14412","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_iScience_Scarpetta.pdf","date_created":"2023-10-09T07:23:46Z","file_size":4872708,"date_updated":"2023-10-09T07:23:46Z","creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"10","volume":26,"ec_funded":1},{"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"}],"abstract":[{"text":"Background: Fighting disease while fighting rivals exposes males to constraints and tradeoffs during male-male competition. We here tested how both the stage and intensity of infection with the fungal pathogen Metarhizium robertsii interfered with fighting success in Cardiocondyla obscurior ant males. Males of this species have evolved long lifespans during which they can gain many matings with the young queens of the colony, if successful in male-male competition. Since male fights occur inside the colony, the outcome of male-male competition can further be biased by interference of the colony’s worker force.\r\nResults: We found that severe, but not yet mild, infection strongly impaired male fighting success. In late-stage infection, this could be attributed to worker aggression directed towards the infected rather than the healthy male and an already very high male morbidity even in the absence of fighting. Shortly after pathogen exposure, however, male mortality was particularly increased during combat. Since these males mounted a strong immune response, their reduced fighting success suggests a trade-off between immune investment and competitive ability already early in the infection. Even if the males themselves showed no difference in the number of attacks they raised against their healthy rivals across infection stages and levels, severely infected males were thus losing in male-male competition from an early stage of infection on.\r\nConclusions: Males of the ant C. obscurior have evolved high immune investment, triggering an effective immune response very fast after fungal exposure. This allows them to cope with mild pathogen exposures without cost to their success in male-male competition, and hence to gain multiple mating opportunities with the emerging virgin queens of the colony. Under severe infection, however, they are weak fighters and rarely survive a combat already at early infection when raising an immune response, as well as at progressed infection, when they are morbid and preferentially targeted by worker aggression. Workers thereby remove males that pose a future disease threat by biasing male-male competition. Our study thus revealed a novel social immunity mechanism how social insect workers protect the colony against disease risk.","lang":"eng"}],"month":"08","intvolume":" 23","scopus_import":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14048","checksum":"95966dc7d242d2c85bdd4fe14233dbd8","creator":"dernst","file_size":2004276,"date_updated":"2023-08-14T07:51:47Z","file_name":"2023_BMCEcology_Metzler.pdf","date_created":"2023-08-14T07:51:47Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2730-7182"]},"publication_status":"published","volume":23,"related_material":{"record":[{"relation":"research_data","id":"12693","status":"public"}]},"ec_funded":1,"_id":"12696","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-12-13T11:13:14Z","file_date_updated":"2023-08-14T07:51:47Z","department":[{"_id":"SyCr"}],"acknowledgement":"We are thankful to Mike Bidochka for the fungal strain, Lukas Schrader for sharing the C. obscurior genome data for primer development, the Lab Support Facility of ISTA for general laboratory support and help with the permit approval procedures, and the Finca El Quinto for letting us collect ants on their property. We thank the Social Immunity Team at ISTA for help with ant collection and experimental help, in particular Elina Hanhimäki and Marta Gorecka for behavioural observation, and Elisabeth Naderlinger for spore load PCRs. We further thank the Social Immunity Team and Jürgen Heinze for continued discussion and comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology Austria (ISTA). This project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 771402 to SC). ","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"07","publication":"BMC Ecology and Evolution","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1186/s12862-023-02137-7","date_published":"2023-08-07T00:00:00Z","date_created":"2023-02-28T07:38:17Z","article_number":"37","project":[{"grant_number":"771402","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Metzler, Sina, Jessica Kirchner, Anna V Grasse, and Sylvia Cremer. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution. Springer Nature, 2023. https://doi.org/10.1186/s12862-023-02137-7.","ista":"Metzler S, Kirchner J, Grasse AV, Cremer S. 2023. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 23, 37.","mla":"Metzler, Sina, et al. “Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males.” BMC Ecology and Evolution, vol. 23, 37, Springer Nature, 2023, doi:10.1186/s12862-023-02137-7.","ama":"Metzler S, Kirchner J, Grasse AV, Cremer S. Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. 2023;23. doi:10.1186/s12862-023-02137-7","apa":"Metzler, S., Kirchner, J., Grasse, A. V., & Cremer, S. (2023). Trade-offs between immunity and competitive ability in fighting ant males. BMC Ecology and Evolution. Springer Nature. https://doi.org/10.1186/s12862-023-02137-7","short":"S. Metzler, J. Kirchner, A.V. Grasse, S. Cremer, BMC Ecology and Evolution 23 (2023).","ieee":"S. Metzler, J. Kirchner, A. V. Grasse, and S. Cremer, “Trade-offs between immunity and competitive ability in fighting ant males,” BMC Ecology and Evolution, vol. 23. Springer Nature, 2023."},"title":"Trade-offs between immunity and competitive ability in fighting ant males","author":[{"last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494","id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina"},{"full_name":"Kirchner, Jessica","last_name":"Kirchner","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","first_name":"Jessica"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"external_id":{"isi":["001042643600002"],"pmid":["37550612"]},"article_processing_charge":"Yes"},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was carried out within the framework of the EV-K2-CNR and Nepal Academy of Science and Technology. K.Y. was supported by the Second Tibetan Plateau Scientific Expedition and Research Program (grant no. 2019QZKK0206). N.C. was supported by the project NODES, which has received funding from the MUR–M4C2 1.5 of PNRR funded by the European Union - NextGeneration EU (Grant agreement no. ECS00000036). T.E.S. has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant no. 101026058. F.P. has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant no. 772751, RAVEN, ‘Rapid mass losses of debris-covered glaciers in High Mountain Asia’ and has been supported by the SNSF grant ‘High-elevation precipitation in High Mountain Asia’ (grant no. 183633). A.A. was supported by the European Union’s Horizon 2020 research and innovation program under grant agreement no. 101004156 (CONFESS project) and by the European Union’s Horizon Europe research and innovation program under grant agreement no. 101081193 (OptimESM project). We thank H. Wehrli for valuable comments and suggestions and J. Giannitrapani for the graphic support. We thank A. Da Polenza and K. Bista of EV-K2-CNR for believing that studying the high elevations is relevant for the whole globe.","date_published":"2023-12-04T00:00:00Z","doi":"10.1038/s41561-023-01331-y","date_created":"2023-12-10T23:00:58Z","page":"1120-1127","day":"04","publication":"Nature Geoscience","has_accepted_license":"1","year":"2023","title":"Local cooling and drying induced by Himalayan glaciers under global warming","author":[{"last_name":"Salerno","full_name":"Salerno, Franco","first_name":"Franco"},{"last_name":"Guyennon","full_name":"Guyennon, Nicolas","first_name":"Nicolas"},{"first_name":"Kun","last_name":"Yang","full_name":"Yang, Kun"},{"last_name":"Shaw","orcid":"0000-0001-7640-6152","full_name":"Shaw, Thomas","id":"3caa3f91-1f03-11ee-96ce-e0e553054d6e","first_name":"Thomas"},{"last_name":"Lin","full_name":"Lin, Changgui","first_name":"Changgui"},{"first_name":"Nicola","full_name":"Colombo, Nicola","last_name":"Colombo"},{"last_name":"Romano","full_name":"Romano, Emanuele","first_name":"Emanuele"},{"last_name":"Gruber","full_name":"Gruber, Stephan","first_name":"Stephan"},{"last_name":"Bolch","full_name":"Bolch, Tobias","first_name":"Tobias"},{"last_name":"Alessandri","full_name":"Alessandri, Andrea","first_name":"Andrea"},{"first_name":"Paolo","last_name":"Cristofanelli","full_name":"Cristofanelli, Paolo"},{"full_name":"Putero, Davide","last_name":"Putero","first_name":"Davide"},{"first_name":"Guglielmina","full_name":"Diolaiuti, Guglielmina","last_name":"Diolaiuti"},{"full_name":"Tartari, Gianni","last_name":"Tartari","first_name":"Gianni"},{"first_name":"Gianpietro","last_name":"Verza","full_name":"Verza, Gianpietro"},{"last_name":"Thakuri","full_name":"Thakuri, Sudeep","first_name":"Sudeep"},{"last_name":"Balsamo","full_name":"Balsamo, Gianpaolo","first_name":"Gianpaolo"},{"full_name":"Miles, Evan S.","last_name":"Miles","first_name":"Evan S."},{"first_name":"Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087"}],"article_processing_charge":"Yes (in subscription journal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Salerno, Franco, Nicolas Guyennon, Kun Yang, Thomas Shaw, Changgui Lin, Nicola Colombo, Emanuele Romano, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience. Springer Nature, 2023. https://doi.org/10.1038/s41561-023-01331-y.","ista":"Salerno F, Guyennon N, Yang K, Shaw T, Lin C, Colombo N, Romano E, Gruber S, Bolch T, Alessandri A, Cristofanelli P, Putero D, Diolaiuti G, Tartari G, Verza G, Thakuri S, Balsamo G, Miles ES, Pellicciotti F. 2023. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 16, 1120–1127.","mla":"Salerno, Franco, et al. “Local Cooling and Drying Induced by Himalayan Glaciers under Global Warming.” Nature Geoscience, vol. 16, Springer Nature, 2023, pp. 1120–27, doi:10.1038/s41561-023-01331-y.","short":"F. Salerno, N. Guyennon, K. Yang, T. Shaw, C. Lin, N. Colombo, E. Romano, S. Gruber, T. Bolch, A. Alessandri, P. Cristofanelli, D. Putero, G. Diolaiuti, G. Tartari, G. Verza, S. Thakuri, G. Balsamo, E.S. Miles, F. Pellicciotti, Nature Geoscience 16 (2023) 1120–1127.","ieee":"F. Salerno et al., “Local cooling and drying induced by Himalayan glaciers under global warming,” Nature Geoscience, vol. 16. Springer Nature, pp. 1120–1127, 2023.","apa":"Salerno, F., Guyennon, N., Yang, K., Shaw, T., Lin, C., Colombo, N., … Pellicciotti, F. (2023). Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. Springer Nature. https://doi.org/10.1038/s41561-023-01331-y","ama":"Salerno F, Guyennon N, Yang K, et al. Local cooling and drying induced by Himalayan glaciers under global warming. Nature Geoscience. 2023;16:1120-1127. doi:10.1038/s41561-023-01331-y"},"month":"12","intvolume":" 16","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Understanding the response of Himalayan glaciers to global warming is vital because of their role as a water source for the Asian subcontinent. However, great uncertainties still exist on the climate drivers of past and present glacier changes across scales. Here, we analyse continuous hourly climate station data from a glacierized elevation (Pyramid station, Mount Everest) since 1994 together with other ground observations and climate reanalysis. We show that a decrease in maximum air temperature and precipitation occurred during the last three decades at Pyramid in response to global warming. Reanalysis data suggest a broader occurrence of this effect in the glacierized areas of the Himalaya. We hypothesize that the counterintuitive cooling is caused by enhanced sensible heat exchange and the associated increase in glacier katabatic wind, which draws cool air downward from higher elevations. The stronger katabatic winds have also lowered the elevation of local wind convergence, thereby diminishing precipitation in glacial areas and negatively affecting glacier mass balance. This local cooling may have partially preserved glaciers from melting and could help protect the periglacial environment."}],"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/wind-of-climate-change/","description":"News on ISTA website"}]},"volume":16,"file":[{"date_created":"2023-12-11T10:11:19Z","file_name":"2023_NatureGeoscience_Salerno.pdf","creator":"dernst","date_updated":"2023-12-11T10:11:19Z","file_size":6072603,"file_id":"14671","checksum":"d5ae0d17069eebc6f454c8608cf83e21","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1752-0908"],"issn":["1752-0894"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14659","department":[{"_id":"FrPe"}],"file_date_updated":"2023-12-11T10:11:19Z","ddc":["550"],"date_updated":"2023-12-13T11:01:10Z"},{"article_number":"1659","citation":{"apa":"Zhang, D., Lape, R., Shaikh, S. A., Kohegyi, B. K., Watson, J., Cais, O., … Greger, I. H. (2023). Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37259-5","ama":"Zhang D, Lape R, Shaikh SA, et al. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 2023;14. doi:10.1038/s41467-023-37259-5","ieee":"D. Zhang et al., “Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"D. Zhang, R. Lape, S.A. Shaikh, B.K. Kohegyi, J. Watson, O. Cais, T. Nakagawa, I.H. Greger, Nature Communications 14 (2023).","mla":"Zhang, Danyang, et al. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications, vol. 14, 1659, Springer Nature, 2023, doi:10.1038/s41467-023-37259-5.","ista":"Zhang D, Lape R, Shaikh SA, Kohegyi BK, Watson J, Cais O, Nakagawa T, Greger IH. 2023. Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics. Nature Communications. 14, 1659.","chicago":"Zhang, Danyang, Remigijus Lape, Saher A. Shaikh, Bianka K. Kohegyi, Jake Watson, Ondrej Cais, Terunaga Nakagawa, and Ingo H. Greger. “Modulatory Mechanisms of TARP Γ8-Selective AMPA Receptor Therapeutics.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37259-5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Zhang, Danyang","last_name":"Zhang","first_name":"Danyang"},{"last_name":"Lape","full_name":"Lape, Remigijus","first_name":"Remigijus"},{"full_name":"Shaikh, Saher A.","last_name":"Shaikh","first_name":"Saher A."},{"first_name":"Bianka K.","last_name":"Kohegyi","full_name":"Kohegyi, Bianka K."},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","first_name":"Jake","last_name":"Watson","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake"},{"last_name":"Cais","full_name":"Cais, Ondrej","first_name":"Ondrej"},{"first_name":"Terunaga","last_name":"Nakagawa","full_name":"Nakagawa, Terunaga"},{"last_name":"Greger","full_name":"Greger, Ingo H.","first_name":"Ingo H."}],"article_processing_charge":"No","external_id":{"isi":["001066658700003"]},"title":"Modulatory mechanisms of TARP γ8-selective AMPA receptor therapeutics","acknowledgement":"We thank James Krieger for generating the ‘proDy’ interaction maps in Fig. 5B and S7C, and Jan-Niklas Dohrke for critically reading the manuscript. We thank members of the Greger lab for insightful comments during this study. We acknowledge Trevor Rutherford for confirming ligand integrity by NMR. We are also grateful to LMB scientific computing and the EM facility for their support. This research was funded in part by the Wellcome Trust (223194/Z/21/Z) to I.H.G. For the purpose of Open Access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Further funding came from the Medical Research Council (MRU105174197) to I.H.G, and NIH grant (R56/R01MH123474) to T.N.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"25","publication":"Nature Communications","doi":"10.1038/s41467-023-37259-5","date_published":"2023-03-25T00:00:00Z","date_created":"2023-04-02T22:01:09Z","_id":"12786","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-12-13T11:15:58Z","ddc":["570"],"file_date_updated":"2023-04-03T06:38:56Z","department":[{"_id":"PeJo"}],"abstract":[{"text":"AMPA glutamate receptors (AMPARs) mediate excitatory neurotransmission throughout the brain. Their signalling is uniquely diversified by brain region-specific auxiliary subunits, providing an opportunity for the development of selective therapeutics. AMPARs associated with TARP γ8 are enriched in the hippocampus, and are targets of emerging anti-epileptic drugs. To understand their therapeutic activity, we determined cryo-EM structures of the GluA1/2-γ8 receptor associated with three potent, chemically diverse ligands. We find that despite sharing a lipid-exposed and water-accessible binding pocket, drug action is differentially affected by binding-site mutants. Together with patch-clamp recordings and MD simulations we also demonstrate that ligand-triggered reorganisation of the AMPAR-TARP interface contributes to modulation. Unexpectedly, one ligand (JNJ-61432059) acts bifunctionally, negatively affecting GluA1 but exerting positive modulatory action on GluA2-containing AMPARs, in a TARP stoichiometry-dependent manner. These results further illuminate the action of TARPs, demonstrate the sensitive balance between positive and negative modulatory action, and provide a mechanistic platform for development of both positive and negative selective AMPAR modulators.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"03","intvolume":" 14","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"success":1,"file_id":"12797","checksum":"0a97b31191432dae5853bbb5ccb7698d","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_NatureComm_Zhang.pdf","date_created":"2023-04-03T06:38:56Z","file_size":2613996,"date_updated":"2023-04-03T06:38:56Z","creator":"dernst"}],"language":[{"iso":"eng"}],"volume":14},{"day":"28","file":[{"file_size":77070,"date_updated":"2023-02-28T06:34:08Z","creator":"scremer","file_name":"Metzler_ReadMe.pdf","date_created":"2023-02-28T06:34:08Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"c1565d655ca05601acfd84e0d12b8563","file_id":"12694"},{"file_name":"Metzler_RepositoryData.xlsx","date_created":"2023-02-28T06:34:12Z","file_size":88001,"date_updated":"2023-02-28T06:34:12Z","creator":"scremer","success":1,"file_id":"12695","checksum":"75c4c4948563d6261cb7548f80d909f1","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","relation":"main_file","access_level":"open_access"}],"has_accepted_license":"1","year":"2023","date_published":"2023-02-28T00:00:00Z","doi":"10.15479/AT:ISTA:12693","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12696"}]},"date_created":"2023-02-28T06:38:37Z","contributor":[{"last_name":"Metzler","first_name":"Sina","contributor_type":"data_collector","id":"48204546-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kirchner","id":"21516227-15aa-11ec-9fb2-c6e8ffc155d3","contributor_type":"data_collector","first_name":"Jessica"},{"contributor_type":"data_collector","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"See Readme File for further information."}],"month":"02","publisher":"Institute of Science and Technology Austria","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"date_updated":"2023-12-13T11:13:13Z","citation":{"mla":"Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.","ama":"Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693","apa":"Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693","short":"S. Cremer, (2023).","ieee":"S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.","chicago":"Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.","ista":"Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693."},"title":"Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ","department":[{"_id":"SyCr"}],"file_date_updated":"2023-02-28T06:34:12Z","author":[{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"article_processing_charge":"No","_id":"12693","status":"public","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"}},{"month":"06","intvolume":" 29","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Urban-living individuals are exposed to many environmental factors that may combine and interact to influence mental health. While individual factors of an urban environment have been investigated in isolation, no attempt has been made to model how complex, real-life exposure to living in the city relates to brain and mental health, and how this is moderated by genetic factors. Using the data of 156,075 participants from the UK Biobank, we carried out sparse canonical correlation analyses to investigate the relationships between urban environments and psychiatric symptoms. We found an environmental profile of social deprivation, air pollution, street network and urban land-use density that was positively correlated with an affective symptom group (r = 0.22, Pperm < 0.001), mediated by brain volume differences consistent with reward processing, and moderated by genes enriched for stress response, including CRHR1, explaining 2.01% of the variance in brain volume differences. Protective factors such as greenness and generous destination accessibility were negatively correlated with an anxiety symptom group (r = 0.10, Pperm < 0.001), mediated by brain regions necessary for emotion regulation and moderated by EXD3, explaining 1.65% of the variance. The third urban environmental profile was correlated with an emotional instability symptom group (r = 0.03, Pperm < 0.001). Our findings suggest that different environmental profiles of urban living may influence specific psychiatric symptom groups through distinct neurobiological pathways."}],"volume":29,"file":[{"file_size":7365360,"date_updated":"2023-06-26T10:15:44Z","creator":"dernst","file_name":"2023_NatureMedicine_Xu.pdf","date_created":"2023-06-26T10:15:44Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"13171","checksum":"bcd3225b2731c3442fa98987fd3bd46d"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1546-170X"],"issn":["1078-8956"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"13168","department":[{"_id":"GaNo"}],"file_date_updated":"2023-06-26T10:15:44Z","ddc":["570"],"date_updated":"2023-12-13T11:25:55Z","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"This work received support from the European Union-funded Horizon Europe project ‘environMENTAL’ (no. 101057429 to G.S., A.M. and M.M.N.) and cofunding by UK Research and Innovation under the UK Government’s Horizon Europe funding guarantee (nos. 10041392 and 10038599) for study design and data analysis; the Horizon 2020-funded European Research Council Advanced Grant ‘STRATIFY’ (no. 695313 to G.S. for study design and data analysis); the Human Brain Project (HBP SGA3, no. 945539 to G.S. for study design and data analysis); the National Institutes of Health (grant no. R01DA049238 to G.S. for study design and data analysis); the German Research Foundation (COPE; grant no. 675346 to G.S. for study design and data analysis); the National Natural Science Foundation of China (grant no. 82001797 to J.X., grant no. 82030053 to C.Y., grant no. 82202093 to J.T. and grant no. 82150710554 to G.S. for study design, data analysis and preparation of the manuscript); National Key Research and Development Program of China (grant no. 2018YFC1314301 to C.Y. for study design and data analysis); Tianjin Applied Basic Research Diversified Investment Foundation (grant no. 21JCYBJC01360 to J.X. for study design and data analysis); Tianjin Health Technology Project (grant no. TJWJ2021QN002 to J.X. for preparation of the manuscript); Science & Technology Development Fund of the Tianjin Education Commission for Higher Education (grant no. 2019KJ195 to J.X. for preparation of the manuscript); the Tianjin Medical University ‘Clinical Talent Training 123 Climbing Plan’ to J.X. for the preparation of the manuscript; Tianjin Key Medical Discipline (Specialty) Construction Project (grant no. TJYXZDXK-001A to C.Y. for preparation of the manuscript); the National Key R&D Program of China (grant no. 2022YFE0209400 to L.Y. for study design and data analysis); the Tsinghua University Initiative Scientific Research Program (grant no. 2021Z11GHX002 to L.Y. for study design and data analysis); the National Key Scientific and Technological Infrastructure Project ‘Earth System Science Numerical Simulator Facility’ (EarthLab to L.Y. for study design and data analysis); the Chinese National High-end Foreign Expert Recruitment Plan to G.S.; and the Alexander von Humboldt Foundation to G.S. for study design and data analysis.","date_published":"2023-06-15T00:00:00Z","doi":"10.1038/s41591-023-02365-w","date_created":"2023-06-25T22:00:46Z","page":"1456-1467","day":"15","publication":"Nature Medicine","has_accepted_license":"1","isi":1,"year":"2023","title":"Effects of urban living environments on mental health in adults","author":[{"last_name":"Xu","full_name":"Xu, Jiayuan","first_name":"Jiayuan"},{"full_name":"Liu, Nana","last_name":"Liu","first_name":"Nana"},{"full_name":"Polemiti, Elli","last_name":"Polemiti","first_name":"Elli"},{"full_name":"Garcia-Mondragon, Liliana","last_name":"Garcia-Mondragon","first_name":"Liliana"},{"full_name":"Tang, Jie","last_name":"Tang","first_name":"Jie"},{"first_name":"Xiaoxuan","last_name":"Liu","full_name":"Liu, Xiaoxuan"},{"first_name":"Tristram","full_name":"Lett, Tristram","last_name":"Lett"},{"first_name":"Le","last_name":"Yu","full_name":"Yu, Le"},{"full_name":"Nöthen, Markus M.","last_name":"Nöthen","first_name":"Markus M."},{"last_name":"Feng","full_name":"Feng, Jianfeng","first_name":"Jianfeng"},{"first_name":"Chunshui","full_name":"Yu, Chunshui","last_name":"Yu"},{"first_name":"Andre","full_name":"Marquand, Andre","last_name":"Marquand"},{"full_name":"Schumann, Gunter","last_name":"Schumann","first_name":"Gunter"},{"first_name":"Henrik","last_name":"Walter","full_name":"Walter, Henrik"},{"first_name":"Andreas","full_name":"Heinz, Andreas","last_name":"Heinz"},{"full_name":"Ralser, Markus","last_name":"Ralser","first_name":"Markus"},{"last_name":"Twardziok","full_name":"Twardziok, Sven","first_name":"Sven"},{"first_name":"Nilakshi","full_name":"Vaidya, Nilakshi","last_name":"Vaidya"},{"first_name":"Emin","full_name":"Serin, Emin","last_name":"Serin"},{"first_name":"Marcel","full_name":"Jentsch, Marcel","last_name":"Jentsch"},{"first_name":"Esther","full_name":"Hitchen, Esther","last_name":"Hitchen"},{"full_name":"Eils, Roland","last_name":"Eils","first_name":"Roland"},{"first_name":"Ulrike Helene","full_name":"Taron, Ulrike Helene","last_name":"Taron"},{"first_name":"Tatjana","full_name":"Schütz, Tatjana","last_name":"Schütz"},{"first_name":"Kerstin","full_name":"Schepanski, Kerstin","last_name":"Schepanski"},{"first_name":"Jamie","last_name":"Banks","full_name":"Banks, Jamie"},{"last_name":"Banaschewski","full_name":"Banaschewski, Tobias","first_name":"Tobias"},{"last_name":"Jansone","full_name":"Jansone, Karina","first_name":"Karina"},{"full_name":"Christmann, Nina","last_name":"Christmann","first_name":"Nina"},{"full_name":"Meyer-Lindenberg, Andreas","last_name":"Meyer-Lindenberg","first_name":"Andreas"},{"full_name":"Tost, Heike","last_name":"Tost","first_name":"Heike"},{"first_name":"Nathalie","last_name":"Holz","full_name":"Holz, Nathalie"},{"first_name":"Emanuel","full_name":"Schwarz, Emanuel","last_name":"Schwarz"},{"first_name":"Argyris","last_name":"Stringaris","full_name":"Stringaris, Argyris"},{"last_name":"Neidhart","full_name":"Neidhart, Maja","first_name":"Maja"},{"last_name":"Nees","full_name":"Nees, Frauke","first_name":"Frauke"},{"full_name":"Siehl, Sebastian","last_name":"Siehl","first_name":"Sebastian"},{"last_name":"A. Andreassen","full_name":"A. Andreassen, Ole","first_name":"Ole"},{"first_name":"Lars","last_name":"T. Westlye","full_name":"T. Westlye, Lars"},{"first_name":"Dennis","last_name":"Van Der Meer","full_name":"Van Der Meer, Dennis"},{"full_name":"Fernandez, Sara","last_name":"Fernandez","first_name":"Sara"},{"last_name":"Kjelkenes","full_name":"Kjelkenes, Rikka","first_name":"Rikka"},{"last_name":"Ask","full_name":"Ask, Helga","first_name":"Helga"},{"last_name":"Rapp","full_name":"Rapp, Michael","first_name":"Michael"},{"last_name":"Tschorn","full_name":"Tschorn, Mira","first_name":"Mira"},{"first_name":"Sarah Jane","last_name":"Böttger","full_name":"Böttger, Sarah Jane"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino"},{"full_name":"Marr, Lena","last_name":"Marr","first_name":"Lena","id":"4406F586-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Slater","full_name":"Slater, Mel","first_name":"Mel"},{"first_name":"Guillem Feixas","last_name":"Viapiana","full_name":"Viapiana, Guillem Feixas"},{"first_name":"Francisco Eiroa","full_name":"Orosa, Francisco Eiroa","last_name":"Orosa"},{"full_name":"Gallego, Jaime","last_name":"Gallego","first_name":"Jaime"},{"first_name":"Alvaro","last_name":"Pastor","full_name":"Pastor, Alvaro"},{"first_name":"Andreas","full_name":"Forstner, Andreas","last_name":"Forstner"},{"last_name":"Hoffmann","full_name":"Hoffmann, Per","first_name":"Per"},{"first_name":"Markus","last_name":"M. Nöthen","full_name":"M. Nöthen, Markus"},{"first_name":"Andreas","full_name":"J. Forstner, Andreas","last_name":"J. Forstner"},{"full_name":"Claus, Isabelle","last_name":"Claus","first_name":"Isabelle"},{"full_name":"Miller, Abbi","last_name":"Miller","first_name":"Abbi"},{"full_name":"Heilmann-Heimbach, Stefanie","last_name":"Heilmann-Heimbach","first_name":"Stefanie"},{"full_name":"Sommer, Peter","last_name":"Sommer","first_name":"Peter"},{"first_name":"Mona","last_name":"Boye","full_name":"Boye, Mona"},{"full_name":"Wilbertz, Johannes","last_name":"Wilbertz","first_name":"Johannes"},{"first_name":"Karen","last_name":"Schmitt","full_name":"Schmitt, Karen"},{"first_name":"Viktor","last_name":"Jirsa","full_name":"Jirsa, Viktor"},{"first_name":"Spase","full_name":"Petkoski, Spase","last_name":"Petkoski"},{"first_name":"Séverine","full_name":"Pitel, Séverine","last_name":"Pitel"},{"last_name":"Otten","full_name":"Otten, Lisa","first_name":"Lisa"},{"full_name":"Athanasiadis, Anastasios Polykarpos","last_name":"Athanasiadis","first_name":"Anastasios Polykarpos"},{"first_name":"Charlie","last_name":"Pearmund","full_name":"Pearmund, Charlie"},{"full_name":"Spanlang, Bernhard","last_name":"Spanlang","first_name":"Bernhard"},{"first_name":"Elena","full_name":"Alvarez, Elena","last_name":"Alvarez"},{"last_name":"Sanchez","full_name":"Sanchez, Mavi","first_name":"Mavi"},{"first_name":"Arantxa","last_name":"Giner","full_name":"Giner, Arantxa"},{"first_name":"Sören","full_name":"Hese, Sören","last_name":"Hese"},{"last_name":"Renner","full_name":"Renner, Paul","first_name":"Paul"},{"last_name":"Jia","full_name":"Jia, Tianye","first_name":"Tianye"},{"full_name":"Gong, Yanting","last_name":"Gong","first_name":"Yanting"},{"last_name":"Xia","full_name":"Xia, Yunman","first_name":"Yunman"},{"first_name":"Xiao","full_name":"Chang, Xiao","last_name":"Chang"},{"last_name":"Calhoun","full_name":"Calhoun, Vince","first_name":"Vince"},{"first_name":"Jingyu","full_name":"Liu, Jingyu","last_name":"Liu"},{"last_name":"Thompson","full_name":"Thompson, Paul","first_name":"Paul"},{"full_name":"Clinton, Nicholas","last_name":"Clinton","first_name":"Nicholas"},{"first_name":"Sylvane","last_name":"Desrivieres","full_name":"Desrivieres, Sylvane"},{"first_name":"Allan","full_name":"H. Young, Allan","last_name":"H. Young"},{"last_name":"Stahl","full_name":"Stahl, Bernd","first_name":"Bernd"},{"first_name":"George","last_name":"Ogoh","full_name":"Ogoh, George"}],"external_id":{"isi":["001013172700001"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Xu J, Liu N, Polemiti E, Garcia-Mondragon L, Tang J, Liu X, Lett T, Yu L, Nöthen MM, Feng J, Yu C, Marquand A, Schumann G, Walter H, Heinz A, Ralser M, Twardziok S, Vaidya N, Serin E, Jentsch M, Hitchen E, Eils R, Taron UH, Schütz T, Schepanski K, Banks J, Banaschewski T, Jansone K, Christmann N, Meyer-Lindenberg A, Tost H, Holz N, Schwarz E, Stringaris A, Neidhart M, Nees F, Siehl S, A. Andreassen O, T. Westlye L, Van Der Meer D, Fernandez S, Kjelkenes R, Ask H, Rapp M, Tschorn M, Böttger SJ, Novarino G, Marr L, Slater M, Viapiana GF, Orosa FE, Gallego J, Pastor A, Forstner A, Hoffmann P, M. Nöthen M, J. Forstner A, Claus I, Miller A, Heilmann-Heimbach S, Sommer P, Boye M, Wilbertz J, Schmitt K, Jirsa V, Petkoski S, Pitel S, Otten L, Athanasiadis AP, Pearmund C, Spanlang B, Alvarez E, Sanchez M, Giner A, Hese S, Renner P, Jia T, Gong Y, Xia Y, Chang X, Calhoun V, Liu J, Thompson P, Clinton N, Desrivieres S, H. Young A, Stahl B, Ogoh G. 2023. Effects of urban living environments on mental health in adults. Nature Medicine. 29, 1456–1467.","chicago":"Xu, Jiayuan, Nana Liu, Elli Polemiti, Liliana Garcia-Mondragon, Jie Tang, Xiaoxuan Liu, Tristram Lett, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine. Springer Nature, 2023. https://doi.org/10.1038/s41591-023-02365-w.","short":"J. Xu, N. Liu, E. Polemiti, L. Garcia-Mondragon, J. Tang, X. Liu, T. Lett, L. Yu, M.M. Nöthen, J. Feng, C. Yu, A. Marquand, G. Schumann, H. Walter, A. Heinz, M. Ralser, S. Twardziok, N. Vaidya, E. Serin, M. Jentsch, E. Hitchen, R. Eils, U.H. Taron, T. Schütz, K. Schepanski, J. Banks, T. Banaschewski, K. Jansone, N. Christmann, A. Meyer-Lindenberg, H. Tost, N. Holz, E. Schwarz, A. Stringaris, M. Neidhart, F. Nees, S. Siehl, O. A. Andreassen, L. T. Westlye, D. Van Der Meer, S. Fernandez, R. Kjelkenes, H. Ask, M. Rapp, M. Tschorn, S.J. Böttger, G. Novarino, L. Marr, M. Slater, G.F. Viapiana, F.E. Orosa, J. Gallego, A. Pastor, A. Forstner, P. Hoffmann, M. M. Nöthen, A. J. Forstner, I. Claus, A. Miller, S. Heilmann-Heimbach, P. Sommer, M. Boye, J. Wilbertz, K. Schmitt, V. Jirsa, S. Petkoski, S. Pitel, L. Otten, A.P. Athanasiadis, C. Pearmund, B. Spanlang, E. Alvarez, M. Sanchez, A. Giner, S. Hese, P. Renner, T. Jia, Y. Gong, Y. Xia, X. Chang, V. Calhoun, J. Liu, P. Thompson, N. Clinton, S. Desrivieres, A. H. Young, B. Stahl, G. Ogoh, Nature Medicine 29 (2023) 1456–1467.","ieee":"J. Xu et al., “Effects of urban living environments on mental health in adults,” Nature Medicine, vol. 29. Springer Nature, pp. 1456–1467, 2023.","ama":"Xu J, Liu N, Polemiti E, et al. Effects of urban living environments on mental health in adults. Nature Medicine. 2023;29:1456-1467. doi:10.1038/s41591-023-02365-w","apa":"Xu, J., Liu, N., Polemiti, E., Garcia-Mondragon, L., Tang, J., Liu, X., … Ogoh, G. (2023). Effects of urban living environments on mental health in adults. Nature Medicine. Springer Nature. https://doi.org/10.1038/s41591-023-02365-w","mla":"Xu, Jiayuan, et al. “Effects of Urban Living Environments on Mental Health in Adults.” Nature Medicine, vol. 29, Springer Nature, 2023, pp. 1456–67, doi:10.1038/s41591-023-02365-w."}},{"department":[{"_id":"BeBi"}],"file_date_updated":"2023-05-16T09:12:05Z","ddc":["004"],"date_updated":"2023-12-13T11:20:00Z","keyword":["reinforcement learning","deposition","control","color","multi-filament"],"status":"public","conference":{"name":"ICRA: International Conference on Robotics and Automation","start_date":"2023-05-29","location":"London, United Kingdom","end_date":"2023-06-02"},"type":"conference","_id":"12976","volume":2023,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"12977","checksum":"daeaa67124777d88487f933ea3f77164","file_size":5367986,"date_updated":"2023-05-16T09:12:05Z","creator":"mpiovarc","file_name":"Liao2023.pdf","date_created":"2023-05-16T09:12:05Z"}],"publication_status":"published","publication_identifier":{"eisbn":["9798350323658"],"issn":["1050-4729"]},"intvolume":" 2023","month":"07","scopus_import":"1","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"3D printing based on continuous deposition of materials, such as filament-based 3D printing, has seen widespread adoption thanks to its versatility in working with a wide range of materials. An important shortcoming of this type of technology is its limited multi-material capabilities. While there are simple hardware designs that enable multi-material printing in principle, the required software is heavily underdeveloped. A typical hardware design fuses together individual materials fed into a single chamber from multiple inlets before they are deposited. This design, however, introduces a time delay between the intended material mixture and its actual deposition. In this work, inspired by diverse path planning research in robotics, we show that this mechanical challenge can be addressed via improved printer control. We propose to formulate the search for optimal multi-material printing policies in a reinforcement\r\nlearning setup. We put forward a simple numerical deposition model that takes into account the non-linear material mixing and delayed material deposition. To validate our system we focus on color fabrication, a problem known for its strict requirements for varying material mixtures at a high spatial frequency. We demonstrate that our learned control policy outperforms state-of-the-art hand-crafted algorithms."}],"title":"Learning deposition policies for fused multi-material 3D printing","article_processing_charge":"No","external_id":{"isi":["001048371104068"]},"author":[{"first_name":"Kang","full_name":"Liao, Kang","last_name":"Liao"},{"full_name":"Tricard, Thibault","last_name":"Tricard","first_name":"Thibault"},{"id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","last_name":"Piovarci"},{"first_name":"Hans-Peter","last_name":"Seidel","full_name":"Seidel, Hans-Peter"},{"full_name":"Babaei, Vahid","last_name":"Babaei","first_name":"Vahid"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. 2023. Learning deposition policies for fused multi-material 3D printing. 2023 IEEE International Conference on Robotics and Automation. ICRA: International Conference on Robotics and Automation vol. 2023, 12345–12352.","chicago":"Liao, Kang, Thibault Tricard, Michael Piovarci, Hans-Peter Seidel, and Vahid Babaei. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” In 2023 IEEE International Conference on Robotics and Automation, 2023:12345–52. IEEE, 2023. https://doi.org/10.1109/ICRA48891.2023.10160465.","ama":"Liao K, Tricard T, Piovarci M, Seidel H-P, Babaei V. Learning deposition policies for fused multi-material 3D printing. In: 2023 IEEE International Conference on Robotics and Automation. Vol 2023. IEEE; 2023:12345-12352. doi:10.1109/ICRA48891.2023.10160465","apa":"Liao, K., Tricard, T., Piovarci, M., Seidel, H.-P., & Babaei, V. (2023). Learning deposition policies for fused multi-material 3D printing. In 2023 IEEE International Conference on Robotics and Automation (Vol. 2023, pp. 12345–12352). London, United Kingdom: IEEE. https://doi.org/10.1109/ICRA48891.2023.10160465","ieee":"K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, and V. Babaei, “Learning deposition policies for fused multi-material 3D printing,” in 2023 IEEE International Conference on Robotics and Automation, London, United Kingdom, 2023, vol. 2023, pp. 12345–12352.","short":"K. Liao, T. Tricard, M. Piovarci, H.-P. Seidel, V. Babaei, in:, 2023 IEEE International Conference on Robotics and Automation, IEEE, 2023, pp. 12345–12352.","mla":"Liao, Kang, et al. “Learning Deposition Policies for Fused Multi-Material 3D Printing.” 2023 IEEE International Conference on Robotics and Automation, vol. 2023, IEEE, 2023, pp. 12345–52, doi:10.1109/ICRA48891.2023.10160465."},"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","name":"Perception-Aware Appearance Fabrication","grant_number":"M03319"}],"date_created":"2023-05-16T09:14:09Z","doi":"10.1109/ICRA48891.2023.10160465","date_published":"2023-07-04T00:00:00Z","page":"12345-12352","publication":"2023 IEEE International Conference on Robotics and Automation","day":"04","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"publisher":"IEEE","quality_controlled":"1","acknowledgement":"This work is graciously supported by FWF Lise Meitner (Grant M 3319). Kang Liao sincerely thank Emiliano Luci, Chunyu Lin, and Yao Zhao for their huge support."},{"intvolume":" 14","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Molecular compatibility between gametes is a prerequisite for successful fertilization. As long as a sperm and egg can recognize and bind each other via their surface proteins, gamete fusion may occur even between members of separate species, resulting in hybrids that can impact speciation. The egg membrane protein Bouncer confers species specificity to gamete interactions between medaka and zebrafish, preventing their cross-fertilization. Here, we leverage this specificity to uncover distinct amino acid residues and N-glycosylation patterns that differentially influence the function of medaka and zebrafish Bouncer and contribute to cross-species incompatibility. Curiously, in contrast to the specificity observed for medaka and zebrafish Bouncer, seahorse and fugu Bouncer are compatible with both zebrafish and medaka sperm, in line with the pervasive purifying selection that dominates Bouncer’s evolution. The Bouncer-sperm interaction is therefore the product of seemingly opposing evolutionary forces that, for some species, restrict fertilization to closely related fish, and for others, allow broad gamete compatibility that enables hybridization.","lang":"eng"}],"volume":14,"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"d6165f41c7f1c2c04b04256ec9f003fb","file_id":"13172","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_NatureComm_Gert.pdf","date_created":"2023-06-26T10:26:04Z","file_size":1555006,"date_updated":"2023-06-26T10:26:04Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"13164","file_date_updated":"2023-06-26T10:26:04Z","department":[{"_id":"FyKo"}],"ddc":["570"],"date_updated":"2023-12-13T11:26:34Z","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Manfred Schartl for sharing RNA-seq data from medaka ovaries and testes prior to publication; Maria Novatchkova for help with RNA-seq analysis; Katharina Lust for advice on medaka techniques; Milan Malinsky for input on Lake Malawi cichlid Bouncer sequences; Felicia Spitzer, Mirjam Binner, and Anna Bandura for help with genotyping; Friedrich Puhl, Kerstin Rattner, Julia Koenig, and Dijana Sunjic for taking care of zebrafish and medaka; and the Pauli lab for helpful discussions about the project and feedback on the manuscript. K.R.B.G. was supported by a DOC Fellowship from the Austrian Academy of Sciences. Work in the Pauli lab was supported by the FWF START program (Y 1031-B28 to A.P.), the ERC CoG 101044495/GaMe, the HFSP Career Development Award (CDA00066/2015 to A.P.), a HFSP Young Investigator Award (RGY0079/2020 to A.P.) and the FWF SFB RNA-Deco (project number F80). The IMP receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). Work by J.S. and Y.M. in this project was supported by the Israel Science Foundation grant 636/21 to Y.M. Work by L.J. was supported by the Swedish Research Council grant 2020-04936 and the Knut and Alice Wallenberg Foundation grant 2018.0042. For the purpose of Open Access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","date_created":"2023-06-25T22:00:45Z","doi":"10.1038/s41467-023-39317-4","date_published":"2023-06-14T00:00:00Z","publication":"Nature Communications","day":"14","year":"2023","isi":1,"has_accepted_license":"1","article_number":"3506","title":"Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries","article_processing_charge":"No","external_id":{"isi":["001048208600023"]},"author":[{"first_name":"Krista R.B.","last_name":"Gert","full_name":"Gert, Krista R.B."},{"last_name":"Panser","full_name":"Panser, Karin","first_name":"Karin"},{"full_name":"Surm, Joachim","last_name":"Surm","first_name":"Joachim"},{"full_name":"Steinmetz, Benjamin S.","last_name":"Steinmetz","first_name":"Benjamin S."},{"first_name":"Alexander","last_name":"Schleiffer","full_name":"Schleiffer, Alexander"},{"last_name":"Jovine","full_name":"Jovine, Luca","first_name":"Luca"},{"first_name":"Yehu","full_name":"Moran, Yehu","last_name":"Moran"},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Andrea","last_name":"Pauli","full_name":"Pauli, Andrea"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Gert, Krista R.B., Karin Panser, Joachim Surm, Benjamin S. Steinmetz, Alexander Schleiffer, Luca Jovine, Yehu Moran, Fyodor Kondrashov, and Andrea Pauli. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39317-4.","ista":"Gert KRB, Panser K, Surm J, Steinmetz BS, Schleiffer A, Jovine L, Moran Y, Kondrashov F, Pauli A. 2023. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 14, 3506.","mla":"Gert, Krista R. B., et al. “Divergent Molecular Signatures in Fish Bouncer Proteins Define Cross-Fertilization Boundaries.” Nature Communications, vol. 14, 3506, Springer Nature, 2023, doi:10.1038/s41467-023-39317-4.","short":"K.R.B. Gert, K. Panser, J. Surm, B.S. Steinmetz, A. Schleiffer, L. Jovine, Y. Moran, F. Kondrashov, A. Pauli, Nature Communications 14 (2023).","ieee":"K. R. B. Gert et al., “Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Gert KRB, Panser K, Surm J, et al. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. 2023;14. doi:10.1038/s41467-023-39317-4","apa":"Gert, K. R. B., Panser, K., Surm, J., Steinmetz, B. S., Schleiffer, A., Jovine, L., … Pauli, A. (2023). Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39317-4"}},{"page":"331-351","date_created":"2023-01-16T11:46:19Z","doi":"10.2140/pjm.2023.325.331","date_published":"2023-11-03T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Pacific Journal of Mathematics","day":"03","oa":1,"publisher":"Mathematical Sciences Publishers","quality_controlled":"1","acknowledgement":"This paper is part of the author’s PhD thesis at Università of Pisa. Moreover, this\r\nproject has received funding from the European Union’s Horizon 2020 research\r\nand innovation programme under the Marie Skłodowska-Curie Grant Agreement\r\nNo. 101034413. I thank the referee for many helpful comments.","external_id":{"arxiv":["2001.02987"],"isi":["001104766900001"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Matteo","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","orcid":"0000-0002-0854-0306","full_name":"Verzobio, Matteo","last_name":"Verzobio"}],"title":"Some effectivity results for primitive divisors of elliptic divisibility sequences","citation":{"chicago":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.325.331.","ista":"Verzobio M. 2023. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 325(2), 331–351.","mla":"Verzobio, Matteo. “Some Effectivity Results for Primitive Divisors of Elliptic Divisibility Sequences.” Pacific Journal of Mathematics, vol. 325, no. 2, Mathematical Sciences Publishers, 2023, pp. 331–51, doi:10.2140/pjm.2023.325.331.","short":"M. Verzobio, Pacific Journal of Mathematics 325 (2023) 331–351.","ieee":"M. Verzobio, “Some effectivity results for primitive divisors of elliptic divisibility sequences,” Pacific Journal of Mathematics, vol. 325, no. 2. Mathematical Sciences Publishers, pp. 331–351, 2023.","ama":"Verzobio M. Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. 2023;325(2):331-351. doi:10.2140/pjm.2023.325.331","apa":"Verzobio, M. (2023). Some effectivity results for primitive divisors of elliptic divisibility sequences. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.325.331"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"ec_funded":1,"volume":325,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["0030-8730"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14525","checksum":"b6218d16a72742d8bb38d6fc3c9bb8c6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_PacificJourMaths_Verzobio.pdf","date_created":"2023-11-13T09:50:41Z","file_size":389897,"date_updated":"2023-11-13T09:50:41Z","creator":"dernst"}],"scopus_import":"1","intvolume":" 325","month":"11","abstract":[{"text":"Let P be a nontorsion point on an elliptic curve defined over a number field K and consider the sequence {Bn}n∈N of the denominators of x(nP). We prove that every term of the sequence of the Bn has a primitive divisor for n greater than an effectively computable constant that we will explicitly compute. This constant will depend only on the model defining the curve.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"TiBr"}],"file_date_updated":"2023-11-13T09:50:41Z","date_updated":"2023-12-13T11:18:14Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"12313"},{"author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo"},{"last_name":"Lytvynov","full_name":"Lytvynov, Eugene","first_name":"Eugene"}],"external_id":{"isi":["001042025400001"]},"article_processing_charge":"No","title":"A Mecke-type characterization of the Dirichlet–Ferguson measure","citation":{"chicago":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-ECP528.","ista":"Dello Schiavo L, Lytvynov E. 2023. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 28, 1–12.","mla":"Dello Schiavo, Lorenzo, and Eugene Lytvynov. “A Mecke-Type Characterization of the Dirichlet–Ferguson Measure.” Electronic Communications in Probability, vol. 28, Institute of Mathematical Statistics, 2023, pp. 1–12, doi:10.1214/23-ECP528.","short":"L. Dello Schiavo, E. Lytvynov, Electronic Communications in Probability 28 (2023) 1–12.","ieee":"L. Dello Schiavo and E. Lytvynov, “A Mecke-type characterization of the Dirichlet–Ferguson measure,” Electronic Communications in Probability, vol. 28. Institute of Mathematical Statistics, pp. 1–12, 2023.","ama":"Dello Schiavo L, Lytvynov E. A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. 2023;28:1-12. doi:10.1214/23-ECP528","apa":"Dello Schiavo, L., & Lytvynov, E. (2023). A Mecke-type characterization of the Dirichlet–Ferguson measure. Electronic Communications in Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-ECP528"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Configuration Spaces over Non-Smooth Spaces","grant_number":"E208","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c"}],"page":"1-12","doi":"10.1214/23-ECP528","date_published":"2023-05-05T00:00:00Z","date_created":"2023-06-18T22:00:48Z","has_accepted_license":"1","isi":1,"year":"2023","day":"05","publication":"Electronic Communications in Probability","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"acknowledgement":"Research supported by the Sfb 1060 The Mathematics of Emergent Effects (University of Bonn). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through project ESPRIT 208.","file_date_updated":"2023-06-19T09:37:40Z","department":[{"_id":"JaMa"}],"date_updated":"2023-12-13T11:24:57Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13145","volume":28,"publication_identifier":{"eissn":["1083-589X"]},"publication_status":"published","file":[{"date_created":"2023-06-19T09:37:40Z","file_name":"2023_ElectronCommProbability_Schiavo.pdf","creator":"dernst","date_updated":"2023-06-19T09:37:40Z","file_size":271434,"checksum":"4a543fe4b3f9e747cc52167c17bfb524","file_id":"13152","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 28","abstract":[{"text":"We prove a characterization of the Dirichlet–Ferguson measure over an arbitrary finite diffuse measure space. We provide an interpretation of this characterization in analogy with the Mecke identity for Poisson point processes.","lang":"eng"}],"oa_version":"Published Version"},{"quality_controlled":"1","publisher":"IEEE","oa":1,"acknowledgement":"YZ thanks Jiajin Li for making the observation given by Equation (23). He also would like to thank Nir Ailon and Ely Porat for several helpful conversations throughout this project, and Alexander Barg for insightful comments on the manuscript.\r\nYZ has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]. The work of SV was supported by a seed grant from IIT Hyderabad and the start-up research grant from the Science and Engineering Research Board, India (SRG/2020/000910).","page":"4513-4527","doi":"10.1109/TIT.2023.3260950","date_published":"2023-07-01T00:00:00Z","date_created":"2023-04-16T22:01:09Z","isi":1,"year":"2023","day":"01","publication":"IEEE Transactions on Information Theory","author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04407"],"isi":["001017307000023"]},"title":"Multiple packing: Lower bounds via infinite constellations","citation":{"mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory, vol. 69, no. 7, IEEE, 2023, pp. 4513–27, doi:10.1109/TIT.2023.3260950.","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 2023;69(7):4513-4527. doi:10.1109/TIT.2023.3260950","apa":"Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3260950","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via infinite constellations,” IEEE Transactions on Information Theory, vol. 69, no. 7. IEEE, pp. 4513–4527, 2023.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 69 (2023) 4513–4527.","chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Infinite Constellations.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3260950.","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via infinite constellations. IEEE Transactions on Information Theory. 69(7), 4513–4527."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04407","open_access":"1"}],"month":"07","intvolume":" 69","abstract":[{"lang":"eng","text":"We study the problem of high-dimensional multiple packing in Euclidean space. Multiple packing is a natural generalization of sphere packing and is defined as follows. Let N > 0 and L ∈ Z ≽2 . A multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L – 1 balls of radius √ nN around points in C . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied for finite fields. In this paper, we derive the best known lower bounds on the optimal density of list-decodable infinite constellations for constant L under a stronger notion called average-radius multiple packing. To this end, we apply tools from high-dimensional geometry and large deviation theory."}],"oa_version":"Preprint","issue":"7","volume":69,"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"12838","department":[{"_id":"MaMo"}],"date_updated":"2023-12-13T11:16:46Z"},{"publication":"FAccT '23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency","day":"12","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-07-16T22:01:09Z","doi":"10.1145/3593013.3594028","date_published":"2023-06-12T00:00:00Z","page":"604-614","acknowledgement":"The authors would like to thank the anonymous reviewers for their valuable comments and helpful suggestions. This work is supported by the European Research Council under Grant No.: ERC-2020-AdG 101020093.","oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Henzinger, T. A., Karimi, M., Kueffner, K., & Mallik, K. (2023). Runtime monitoring of dynamic fairness properties. In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency (pp. 604–614). Chicago, IL, United States: Association for Computing Machinery. https://doi.org/10.1145/3593013.3594028","ama":"Henzinger TA, Karimi M, Kueffner K, Mallik K. Runtime monitoring of dynamic fairness properties. In: FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. Association for Computing Machinery; 2023:604-614. doi:10.1145/3593013.3594028","ieee":"T. A. Henzinger, M. Karimi, K. Kueffner, and K. Mallik, “Runtime monitoring of dynamic fairness properties,” in FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Chicago, IL, United States, 2023, pp. 604–614.","short":"T.A. Henzinger, M. Karimi, K. Kueffner, K. Mallik, in:, FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–614.","mla":"Henzinger, Thomas A., et al. “Runtime Monitoring of Dynamic Fairness Properties.” FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, Association for Computing Machinery, 2023, pp. 604–14, doi:10.1145/3593013.3594028.","ista":"Henzinger TA, Karimi M, Kueffner K, Mallik K. 2023. Runtime monitoring of dynamic fairness properties. FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency. FAccT: Conference on Fairness, Accountability and Transparency, 604–614.","chicago":"Henzinger, Thomas A, Mahyar Karimi, Konstantin Kueffner, and Kaushik Mallik. “Runtime Monitoring of Dynamic Fairness Properties.” In FAccT ’23: Proceedings of the 2023 ACM Conference on Fairness, Accountability, and Transparency, 604–14. Association for Computing Machinery, 2023. https://doi.org/10.1145/3593013.3594028."},"title":"Runtime monitoring of dynamic fairness properties","article_processing_charge":"No","external_id":{"arxiv":["2305.04699"],"isi":["001062819300057"]},"author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Karimi, Mahyar","last_name":"Karimi","first_name":"Mahyar"},{"id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin","last_name":"Kueffner","full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542"},{"full_name":"Mallik, Kaushik","orcid":"0000-0001-9864-7475","last_name":"Mallik","first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"}],"project":[{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13245","checksum":"96c759db9cdf94b81e37871a66a6ff48","success":1,"date_updated":"2023-07-18T07:43:10Z","file_size":4100596,"creator":"dernst","date_created":"2023-07-18T07:43:10Z","file_name":"2023_ACM_HenzingerT.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9781450372527"]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A machine-learned system that is fair in static decision-making tasks may have biased societal impacts in the long-run. This may happen when the system interacts with humans and feedback patterns emerge, reinforcing old biases in the system and creating new biases. While existing works try to identify and mitigate long-run biases through smart system design, we introduce techniques for monitoring fairness in real time. Our goal is to build and deploy a monitor that will continuously observe a long sequence of events generated by the system in the wild, and will output, with each event, a verdict on how fair the system is at the current point in time. The advantages of monitoring are two-fold. Firstly, fairness is evaluated at run-time, which is important because unfair behaviors may not be eliminated a priori, at design-time, due to partial knowledge about the system and the environment, as well as uncertainties and dynamic changes in the system and the environment, such as the unpredictability of human behavior. Secondly, monitors are by design oblivious to how the monitored system is constructed, which makes them suitable to be used as trusted third-party fairness watchdogs. They function as computationally lightweight statistical estimators, and their correctness proofs rely on the rigorous analysis of the stochastic process that models the assumptions about the underlying dynamics of the system. We show, both in theory and experiments, how monitors can warn us (1) if a bank’s credit policy over time has created an unfair distribution of credit scores among the population, and (2) if a resource allocator’s allocation policy over time has made unfair allocations. Our experiments demonstrate that the monitors introduce very low overhead. We believe that runtime monitoring is an important and mathematically rigorous new addition to the fairness toolbox."}],"month":"06","scopus_import":"1","ddc":["000"],"date_updated":"2023-12-13T11:30:31Z","file_date_updated":"2023-07-18T07:43:10Z","department":[{"_id":"ToHe"}],"_id":"13228","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"end_date":"2023-06-15","location":"Chicago, IL, United States","start_date":"2023-06-12","name":"FAccT: Conference on Fairness, Accountability and Transparency"},"type":"conference"},{"_id":"13225","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-12-13T11:31:14Z","file_date_updated":"2023-11-14T13:12:12Z","department":[{"_id":"RoSe"}],"oa_version":"Published Version","abstract":[{"text":"Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.","lang":"eng"}],"intvolume":" 247","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14535","checksum":"2b45828d854a253b14bf7aa196ec55e9","success":1,"date_updated":"2023-11-14T13:12:12Z","file_size":851626,"creator":"dernst","date_created":"2023-11-14T13:12:12Z","file_name":"2023_ArchiveRationalMechAnalysis_Benedikter.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"ec_funded":1,"issue":"4","volume":247,"article_number":"65","project":[{"call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65.","chicago":"Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01893-6.","short":"N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023).","ieee":"N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” Archive for Rational Mechanics and Analysis, vol. 247, no. 4. Springer Nature, 2023.","apa":"Benedikter, N. P., Porta, M., Schlein, B., & Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01893-6","ama":"Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 2023;247(4). doi:10.1007/s00205-023-01893-6","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” Archive for Rational Mechanics and Analysis, vol. 247, no. 4, 65, Springer Nature, 2023, doi:10.1007/s00205-023-01893-6."},"title":"Correlation energy of a weakly interacting Fermi gas with large interaction potential","article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2106.13185"],"isi":["001024369000001"]},"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","first_name":"Niels P","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter"},{"last_name":"Porta","full_name":"Porta, Marcello","first_name":"Marcello"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"acknowledgement":"RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Archive for Rational Mechanics and Analysis","day":"01","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-07-16T22:01:08Z","doi":"10.1007/s00205-023-01893-6","date_published":"2023-08-01T00:00:00Z"},{"intvolume":" 113","month":"07","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.","lang":"eng"}],"ec_funded":1,"volume":113,"issue":"4","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"status":"public","type":"journal_article","article_type":"original","_id":"13226","department":[{"_id":"RoSe"}],"date_updated":"2023-12-13T11:31:50Z","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL.","date_created":"2023-07-16T22:01:08Z","doi":"10.1007/s11005-023-01698-4","date_published":"2023-07-03T00:00:00Z","publication":"Letters in Mathematical Physics","day":"03","year":"2023","isi":1,"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"article_number":"77","title":"Weak Edgeworth expansion for the mean-field Bose gas","external_id":{"isi":["001022878900002"],"arxiv":["2208.00199"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Bossmann, Lea","orcid":"0000-0002-6854-1343","last_name":"Bossmann","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","first_name":"Lea"},{"last_name":"Petrat","orcid":"0000-0002-9166-5889","full_name":"Petrat, Sören P","first_name":"Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).","ieee":"L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” Letters in Mathematical Physics, vol. 113, no. 4. Springer Nature, 2023.","apa":"Bossmann, L., & Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s11005-023-01698-4","ama":"Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 2023;113(4). doi:10.1007/s11005-023-01698-4","mla":"Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics, vol. 113, no. 4, 77, Springer Nature, 2023, doi:10.1007/s11005-023-01698-4.","ista":"Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77.","chicago":"Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” Letters in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s11005-023-01698-4."}},{"acknowledgement":"The authors thank J. Koch for discussions and support with the scQubits python package, I. Rozhansky and A. Poddubny for important insights into photon-assisted tunneling, S. Barzanjeh and G. Arnold for theory, E. Redchenko, S. Pepic, the MIBA workshop and the IST nanofabrication facility for technical contributions, as well as L. Drmic, P. Zielinski and R. Sett for software development. We acknowledge the prompt support of Quantum Machines to implement active state preparation with their OPX+. This work was supported by a NOMIS foundation research grant (J.F.), the Austrian Science Fund (FWF) through BeyondC F7105 (J.F.) and IST Austria.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","publication":"Nature Communications","day":"05","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-07-16T22:01:08Z","doi":"10.1038/s41467-023-39656-2","date_published":"2023-07-05T00:00:00Z","article_number":"3968","project":[{"call_identifier":"FWF","_id":"26927A52-B435-11E9-9278-68D0E5697425","grant_number":"F07105","name":"Integrating superconducting quantum circuits"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"2622978C-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Hassani, Farid, Matilda Peruzzo, Lucky Kapoor, Andrea Trioni, Martin Zemlicka, and Johannes M Fink. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39656-2.","ista":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. 2023. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 14, 3968.","mla":"Hassani, Farid, et al. “Inductively Shunted Transmons Exhibit Noise Insensitive Plasmon States and a Fluxon Decay Exceeding 3 Hours.” Nature Communications, vol. 14, 3968, Springer Nature, 2023, doi:10.1038/s41467-023-39656-2.","apa":"Hassani, F., Peruzzo, M., Kapoor, L., Trioni, A., Zemlicka, M., & Fink, J. M. (2023). Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39656-2","ama":"Hassani F, Peruzzo M, Kapoor L, Trioni A, Zemlicka M, Fink JM. Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours. Nature Communications. 2023;14. doi:10.1038/s41467-023-39656-2","ieee":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, and J. M. Fink, “Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"F. Hassani, M. Peruzzo, L. Kapoor, A. Trioni, M. Zemlicka, J.M. Fink, Nature Communications 14 (2023)."},"title":"Inductively shunted transmons exhibit noise insensitive plasmon states and a fluxon decay exceeding 3 hours","external_id":{"isi":["001024729900009"],"pmid":["37407570"]},"article_processing_charge":"No","author":[{"orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","last_name":"Hassani","first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda","last_name":"Peruzzo"},{"id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky","full_name":"Kapoor, Lucky","last_name":"Kapoor"},{"full_name":"Trioni, Andrea","last_name":"Trioni","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zemlicka","full_name":"Zemlicka, Martin","first_name":"Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","last_name":"Fink","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Currently available quantum processors are dominated by noise, which severely limits their applicability and motivates the search for new physical qubit encodings. In this work, we introduce the inductively shunted transmon, a weakly flux-tunable superconducting qubit that offers charge offset protection for all levels and a 20-fold reduction in flux dispersion compared to the state-of-the-art resulting in a constant coherence over a full flux quantum. The parabolic confinement provided by the inductive shunt as well as the linearity of the geometric superinductor facilitates a high-power readout that resolves quantum jumps with a fidelity and QND-ness of >90% and without the need for a Josephson parametric amplifier. Moreover, the device reveals quantum tunneling physics between the two prepared fluxon ground states with a measured average decay time of up to 3.5 h. In the future, fast time-domain control of the transition matrix elements could offer a new path forward to also achieve full qubit control in the decay-protected fluxon basis.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"intvolume":" 14","month":"07","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-07-18T08:43:07Z","file_name":"2023_NatureComm_Hassani.pdf","creator":"dernst","date_updated":"2023-07-18T08:43:07Z","file_size":2899592,"file_id":"13248","checksum":"a85773b5fe23516f60f7d5d31b55c200","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"volume":14,"_id":"13227","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["530"],"date_updated":"2023-12-13T11:32:25Z","file_date_updated":"2023-07-18T08:43:07Z","department":[{"_id":"JoFi"}]},{"acknowledgement":"Marco Mondelli was partially supported by the 2019 Lopez-Loreta prize.","quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","oa":1,"isi":1,"year":"2023","day":"01","publication":"2023 IEEE Information Theory Workshop","page":"294-298","doi":"10.1109/ITW55543.2023.10160238","date_published":"2023-05-01T00:00:00Z","date_created":"2023-07-30T22:01:04Z","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"citation":{"ista":"Xu Y, Hou TQ, Liang SS, Mondelli M. 2023. Approximate message passing for multi-layer estimation in rotationally invariant models. 2023 IEEE Information Theory Workshop. ITW: Information Theory Workshop, 294–298.","chicago":"Xu, Yizhou, Tian Qi Hou, Shan Suo Liang, and Marco Mondelli. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” In 2023 IEEE Information Theory Workshop, 294–98. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/ITW55543.2023.10160238.","ieee":"Y. Xu, T. Q. Hou, S. S. Liang, and M. Mondelli, “Approximate message passing for multi-layer estimation in rotationally invariant models,” in 2023 IEEE Information Theory Workshop, Saint-Malo, France, 2023, pp. 294–298.","short":"Y. Xu, T.Q. Hou, S.S. Liang, M. Mondelli, in:, 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–298.","apa":"Xu, Y., Hou, T. Q., Liang, S. S., & Mondelli, M. (2023). Approximate message passing for multi-layer estimation in rotationally invariant models. In 2023 IEEE Information Theory Workshop (pp. 294–298). Saint-Malo, France: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/ITW55543.2023.10160238","ama":"Xu Y, Hou TQ, Liang SS, Mondelli M. Approximate message passing for multi-layer estimation in rotationally invariant models. In: 2023 IEEE Information Theory Workshop. Institute of Electrical and Electronics Engineers; 2023:294-298. doi:10.1109/ITW55543.2023.10160238","mla":"Xu, Yizhou, et al. “Approximate Message Passing for Multi-Layer Estimation in Rotationally Invariant Models.” 2023 IEEE Information Theory Workshop, Institute of Electrical and Electronics Engineers, 2023, pp. 294–98, doi:10.1109/ITW55543.2023.10160238."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Xu","full_name":"Xu, Yizhou","first_name":"Yizhou"},{"full_name":"Hou, Tian Qi","last_name":"Hou","first_name":"Tian Qi"},{"last_name":"Liang","full_name":"Liang, Shan Suo","first_name":"Shan Suo"},{"first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"}],"article_processing_charge":"No","external_id":{"isi":["001031733100053"],"arxiv":["2212.01572"]},"title":"Approximate message passing for multi-layer estimation in rotationally invariant models","abstract":[{"text":"We consider the problem of reconstructing the signal and the hidden variables from observations coming from a multi-layer network with rotationally invariant weight matrices. The multi-layer structure models inference from deep generative priors, and the rotational invariance imposed on the weights generalizes the i.i.d. Gaussian assumption by allowing for a complex correlation structure, which is typical in applications. In this work, we present a new class of approximate message passing (AMP) algorithms and give a state evolution recursion which precisely characterizes their performance in the large system limit. In contrast with the existing multi-layer VAMP (ML-VAMP) approach, our proposed AMP – dubbed multilayer rotationally invariant generalized AMP (ML-RI-GAMP) – provides a natural generalization beyond Gaussian designs, in the sense that it recovers the existing Gaussian AMP as a special case. Furthermore, ML-RI-GAMP exhibits a significantly lower complexity than ML-VAMP, as the computationally intensive singular value decomposition is replaced by an estimation of the moments of the design matrices. Finally, our numerical results show that this complexity gain comes at little to no cost in the performance of the algorithm.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2212.01572"}],"month":"05","publication_identifier":{"isbn":["9798350301496"],"eissn":["2475-4218"]},"publication_status":"published","language":[{"iso":"eng"}],"_id":"13321","type":"conference","conference":{"name":"ITW: Information Theory Workshop","start_date":"2023-04-23","location":"Saint-Malo, France","end_date":"2023-04-28"},"status":"public","date_updated":"2023-12-13T11:35:46Z","department":[{"_id":"MaMo"}]},{"oa":1,"publisher":"Association for Computing Machinery","quality_controlled":"1","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","date_created":"2023-07-23T22:01:13Z","date_published":"2023-03-17T00:00:00Z","doi":"10.1145/3575859","publication":"ACM Transactions on Graphics","day":"17","year":"2023","isi":1,"article_number":"26","title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]},"article_processing_charge":"No","author":[{"full_name":"Zhong, Fanchao","last_name":"Zhong","first_name":"Fanchao"},{"first_name":"Yonglai","last_name":"Xu","full_name":"Xu, Yonglai"},{"last_name":"Zhao","orcid":"0000-0002-6389-1045","full_name":"Zhao, Haisen","first_name":"Haisen","id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4"},{"first_name":"Lin","full_name":"Lu, Lin","last_name":"Lu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:10.1145/3575859.","ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” ACM Transactions on Graphics, vol. 42, no. 3. Association for Computing Machinery, 2023.","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 2023;42(3). doi:10.1145/3575859","apa":"Zhong, F., Xu, Y., Zhao, H., & Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3575859","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3575859.","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26."},"intvolume":" 42","month":"03","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.02374","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality."}],"volume":42,"issue":"3","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"status":"public","article_type":"original","type":"journal_article","_id":"13265","department":[{"_id":"BeBi"}],"date_updated":"2023-12-13T11:34:59Z"},{"status":"public","type":"journal_article","article_type":"original","_id":"13318","department":[{"_id":"JaMa"}],"date_updated":"2023-12-13T11:36:20Z","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-023-02680-0"}],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Bohnenblust–Hille inequalities for Boolean cubes have been proven with dimension-free constants that grow subexponentially in the degree (Defant et al. in Math Ann 374(1):653–680, 2019). Such inequalities have found great applications in learning low-degree Boolean functions (Eskenazis and Ivanisvili in Proceedings of the 54th annual ACM SIGACT symposium on theory of computing, pp 203–207, 2022). Motivated by learning quantum observables, a qubit analogue of Bohnenblust–Hille inequality for Boolean cubes was recently conjectured in Rouzé et al. (Quantum Talagrand, KKL and Friedgut’s theorems and the learnability of quantum Boolean functions, 2022. arXiv preprint arXiv:2209.07279). The conjecture was resolved in Huang et al. (Learning to predict arbitrary quantum processes, 2022. arXiv preprint arXiv:2210.14894). In this paper, we give a new proof of these Bohnenblust–Hille inequalities for qubit system with constants that are dimension-free and of exponential growth in the degree. As a consequence, we obtain a junta theorem for low-degree polynomials. Using similar ideas, we also study learning problems of low degree quantum observables and Bohr’s radius phenomenon on quantum Boolean cubes."}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"project":[{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","name":"Curvature-dimension in noncommutative analysis","grant_number":"M03337"}],"title":"Noncommutative Bohnenblust–Hille inequalities","article_processing_charge":"No","external_id":{"arxiv":["2210.14468"],"isi":["001035665500001"]},"author":[{"full_name":"Volberg, Alexander","last_name":"Volberg","first_name":"Alexander"},{"last_name":"Zhang","full_name":"Zhang, Haonan","first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen, Springer Nature, 2023, doi:10.1007/s00208-023-02680-0.","ama":"Volberg A, Zhang H. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. 2023. doi:10.1007/s00208-023-02680-0","apa":"Volberg, A., & Zhang, H. (2023). Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-023-02680-0","short":"A. Volberg, H. Zhang, Mathematische Annalen (2023).","ieee":"A. Volberg and H. Zhang, “Noncommutative Bohnenblust–Hille inequalities,” Mathematische Annalen. Springer Nature, 2023.","chicago":"Volberg, Alexander, and Haonan Zhang. “Noncommutative Bohnenblust–Hille Inequalities.” Mathematische Annalen. Springer Nature, 2023. https://doi.org/10.1007/s00208-023-02680-0.","ista":"Volberg A, Zhang H. 2023. Noncommutative Bohnenblust–Hille inequalities. Mathematische Annalen."},"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"The research of A.V. is supported by NSF DMS-1900286, DMS-2154402 and by Hausdorff Center for Mathematics. H.Z. is supported by the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337. This work is partially supported by NSF DMS-1929284 while both authors were in residence at the Institute for Computational and Experimental Research in Mathematics in Providence, RI, during the Harmonic Analysis and Convexity program.","date_created":"2023-07-30T22:01:03Z","date_published":"2023-07-24T00:00:00Z","doi":"10.1007/s00208-023-02680-0","publication":"Mathematische Annalen","day":"24","year":"2023","isi":1},{"publication":"Annales Henri Poincare","day":"08","year":"2023","isi":1,"date_created":"2023-07-23T22:01:15Z","doi":"10.1007/s00023-023-01345-7","date_published":"2023-07-08T00:00:00Z","acknowledgement":"I am grateful to Boguslaw Zegarliński for asking me the questions in [3] and for helpful communication. I also want to thank Paata Ivanisvili for drawing [25] to my attention and for useful correspondence. Many thanks to the anonymous referee for the valuable comments and for pointing out some errors in an earlier version of the paper. This work is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411 and the Lise Meitner fellowship, Austrian Science Fund (FWF) M3337.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare. Springer Nature, 2023. https://doi.org/10.1007/s00023-023-01345-7.","ista":"Zhang H. 2023. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare.","mla":"Zhang, Haonan. “Some Convexity and Monotonicity Results of Trace Functionals.” Annales Henri Poincare, Springer Nature, 2023, doi:10.1007/s00023-023-01345-7.","short":"H. Zhang, Annales Henri Poincare (2023).","ieee":"H. Zhang, “Some convexity and monotonicity results of trace functionals,” Annales Henri Poincare. Springer Nature, 2023.","ama":"Zhang H. Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. 2023. doi:10.1007/s00023-023-01345-7","apa":"Zhang, H. (2023). Some convexity and monotonicity results of trace functionals. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-023-01345-7"},"title":"Some convexity and monotonicity results of trace functionals","external_id":{"arxiv":["2108.05785"],"isi":["001025709100001"]},"article_processing_charge":"No","author":[{"id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","first_name":"Haonan","full_name":"Zhang, Haonan","last_name":"Zhang"}],"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"_id":"eb958bca-77a9-11ec-83b8-c565cb50d8d6","grant_number":"M03337","name":"Curvature-dimension in noncommutative analysis"}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1424-0637"]},"ec_funded":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s,\r\nfor parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems."}],"month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.05785"}],"scopus_import":"1","date_updated":"2023-12-13T11:33:46Z","department":[{"_id":"JaMa"}],"_id":"13271","status":"public","article_type":"original","type":"journal_article"},{"status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"13258","file_date_updated":"2023-07-31T11:32:36Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2023-12-13T11:42:38Z","month":"07","intvolume":" 14","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation."}],"volume":14,"related_material":{"record":[{"id":"13336","status":"public","relation":"research_data"}]},"ec_funded":1,"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5aceefdfe76686267b93ae4fe81899f1","file_id":"13337","success":1,"date_updated":"2023-07-31T11:32:36Z","file_size":1601682,"creator":"dernst","date_created":"2023-07-31T11:32:36Z","file_name":"2023_NatureComm_Kleshnina.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"article_number":"4153","title":"The effect of environmental information on evolution of cooperation in stochastic games","author":[{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6687-1210","full_name":"Simsa, Stepan","last_name":"Simsa","first_name":"Stepan","id":"409d615c-2f95-11ee-b934-90a352102c1e"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin A.","last_name":"Nowak","first_name":"Martin A."}],"external_id":{"isi":["001029450400031"],"pmid":["37438341"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-39625-9.","apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., & Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-39625-9","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 2023;14. doi:10.1038/s41467-023-39625-9","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Nature Communications, vol. 14, 4153, Springer Nature, 2023, doi:10.1038/s41467-023-39625-9."},"quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","doi":"10.1038/s41467-023-39625-9","date_published":"2023-07-12T00:00:00Z","date_created":"2023-07-23T22:01:11Z","day":"12","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2023"},{"project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"title":"Trap spaces of multi-valued networks: Definition, computation, and applications","external_id":{"isi":["001027457000060"],"pmid":["37387165"]},"article_processing_charge":"Yes","author":[{"first_name":"Van Giang","last_name":"Trinh","full_name":"Trinh, Van Giang"},{"last_name":"Benhamou","full_name":"Benhamou, Belaid","first_name":"Belaid"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724"},{"orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel","last_name":"Pastva","first_name":"Samuel","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” Bioinformatics, vol. 39, no. Supplement_1. Oxford Academic, pp. i513–i522, 2023.","short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 2023;39(Supplement_1):i513-i522. doi:10.1093/bioinformatics/btad262","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., & Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. Oxford Academic. https://doi.org/10.1093/bioinformatics/btad262","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics, vol. 39, no. Supplement_1, Oxford Academic, 2023, pp. i513–22, doi:10.1093/bioinformatics/btad262.","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522.","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” Bioinformatics. Oxford Academic, 2023. https://doi.org/10.1093/bioinformatics/btad262."},"oa":1,"quality_controlled":"1","publisher":"Oxford Academic","acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","date_created":"2023-07-23T22:01:12Z","doi":"10.1093/bioinformatics/btad262","date_published":"2023-06-30T00:00:00Z","page":"i513-i522","publication":"Bioinformatics","day":"30","year":"2023","has_accepted_license":"1","isi":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13263","file_date_updated":"2023-07-31T11:09:05Z","department":[{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2023-12-13T11:41:52Z","intvolume":" 39","month":"06","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models."}],"ec_funded":1,"volume":39,"related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"issue":"Supplement_1","language":[{"iso":"eng"}],"file":[{"date_created":"2023-07-31T11:09:05Z","file_name":"2023_Bioinformatics_Trinh.pdf","creator":"dernst","date_updated":"2023-07-31T11:09:05Z","file_size":641736,"checksum":"ba3abe1171df1958413b7c7f957f5486","file_id":"13335","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["1367-4803"],"eissn":["1367-4811"]}},{"scopus_import":"1","month":"07","intvolume":" 12","abstract":[{"text":"Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"volume":12,"publication_identifier":{"eissn":["2050-084X"]},"publication_status":"published","file":[{"success":1,"file_id":"13324","checksum":"2af111a00cf5e3a956f7f0fd13199b15","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_eLife_Toshima.pdf","date_created":"2023-07-31T07:43:00Z","file_size":11980913,"date_updated":"2023-07-31T07:43:00Z","creator":"dernst"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13316","file_date_updated":"2023-07-31T07:43:00Z","department":[{"_id":"DaSi"}],"date_updated":"2023-12-13T11:37:36Z","ddc":["570"],"quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"acknowledgement":"This work was supported by JSPS KAKENHI grant #18K062291, and the Takeda Science Foundation to JYT., as well as JSPS KAKENHI grant #19K065710, the Takeda Science Foundation, and Life Science Foundation of Japan to JT.","date_published":"2023-07-21T00:00:00Z","doi":"10.7554/eLife.84850","date_created":"2023-07-30T22:01:02Z","has_accepted_license":"1","isi":1,"year":"2023","day":"21","publication":"eLife","article_number":"e84850","author":[{"full_name":"Toshima, Junko Y.","last_name":"Toshima","first_name":"Junko Y."},{"first_name":"Ayana","full_name":"Tsukahara, Ayana","last_name":"Tsukahara"},{"first_name":"Makoto","last_name":"Nagano","full_name":"Nagano, Makoto"},{"full_name":"Tojima, Takuro","last_name":"Tojima","first_name":"Takuro"},{"last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nakano","full_name":"Nakano, Akihiko","first_name":"Akihiko"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"external_id":{"isi":["001035372800001"],"pmid":["37477116"]},"article_processing_charge":"Yes","title":"The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network","citation":{"mla":"Toshima, Junko Y., et al. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife, vol. 12, e84850, eLife Sciences Publications, 2023, doi:10.7554/eLife.84850.","ama":"Toshima JY, Tsukahara A, Nagano M, et al. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 2023;12. doi:10.7554/eLife.84850","apa":"Toshima, J. Y., Tsukahara, A., Nagano, M., Tojima, T., Siekhaus, D. E., Nakano, A., & Toshima, J. (2023). The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.84850","ieee":"J. Y. Toshima et al., “The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network,” eLife, vol. 12. eLife Sciences Publications, 2023.","short":"J.Y. Toshima, A. Tsukahara, M. Nagano, T. Tojima, D.E. Siekhaus, A. Nakano, J. Toshima, ELife 12 (2023).","chicago":"Toshima, Junko Y., Ayana Tsukahara, Makoto Nagano, Takuro Tojima, Daria E Siekhaus, Akihiko Nakano, and Jiro Toshima. “The Yeast Endocytic Early/Sorting Compartment Exists as an Independent Sub-Compartment within the Trans-Golgi Network.” ELife. eLife Sciences Publications, 2023. https://doi.org/10.7554/eLife.84850.","ista":"Toshima JY, Tsukahara A, Nagano M, Tojima T, Siekhaus DE, Nakano A, Toshima J. 2023. The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network. eLife. 12, e84850."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13317","file_date_updated":"2023-07-31T07:49:31Z","department":[{"_id":"LaEr"}],"date_updated":"2023-12-13T11:38:44Z","ddc":["510","530"],"scopus_import":"1","intvolume":" 190","month":"07","abstract":[{"text":"We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"7","volume":190,"publication_status":"published","publication_identifier":{"eissn":["1572-9613"],"issn":["0022-4715"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2023-07-31T07:49:31Z","file_size":612755,"creator":"dernst","date_created":"2023-07-31T07:49:31Z","file_name":"2023_JourStatPhysics_Sugimoto.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13325","checksum":"c2ef6b2aecfee1ad6d03fab620507c2c","success":1}],"project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"article_number":"128","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001035677200002"],"arxiv":["2304.04213"]},"author":[{"first_name":"Shoki","last_name":"Sugimoto","full_name":"Sugimoto, Shoki"},{"last_name":"Henheik","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","first_name":"Sven Joscha","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb"},{"full_name":"Riabov, Volodymyr","last_name":"Riabov","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","first_name":"Volodymyr"},{"full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László"}],"title":"Eigenstate thermalisation hypothesis for translation invariant spin systems","citation":{"ista":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. 2023. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 190(7), 128.","chicago":"Sugimoto, Shoki, Sven Joscha Henheik, Volodymyr Riabov, and László Erdös. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics. Springer Nature, 2023. https://doi.org/10.1007/s10955-023-03132-4.","ama":"Sugimoto S, Henheik SJ, Riabov V, Erdös L. Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. 2023;190(7). doi:10.1007/s10955-023-03132-4","apa":"Sugimoto, S., Henheik, S. J., Riabov, V., & Erdös, L. (2023). Eigenstate thermalisation hypothesis for translation invariant spin systems. Journal of Statistical Physics. Springer Nature. https://doi.org/10.1007/s10955-023-03132-4","ieee":"S. Sugimoto, S. J. Henheik, V. Riabov, and L. Erdös, “Eigenstate thermalisation hypothesis for translation invariant spin systems,” Journal of Statistical Physics, vol. 190, no. 7. Springer Nature, 2023.","short":"S. Sugimoto, S.J. Henheik, V. Riabov, L. Erdös, Journal of Statistical Physics 190 (2023).","mla":"Sugimoto, Shoki, et al. “Eigenstate Thermalisation Hypothesis for Translation Invariant Spin Systems.” Journal of Statistical Physics, vol. 190, no. 7, 128, Springer Nature, 2023, doi:10.1007/s10955-023-03132-4."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"LE, JH, and VR were supported by ERC Advanced Grant “RMTBeyond” No. 101020331. SS was supported by KAKENHI Grant Number JP22J14935 from the Japan Society for the Promotion of Science (JSPS) and Forefront Physics and Mathematics Program to Drive Transformation (FoPM), a World-leading Innovative Graduate Study (WINGS) Program, the University of Tokyo.\r\nOpen access funding provided by The University of Tokyo.","date_created":"2023-07-30T22:01:02Z","doi":"10.1007/s10955-023-03132-4","date_published":"2023-07-21T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Journal of Statistical Physics","day":"21"},{"issue":"1","volume":14,"publication_identifier":{"issn":["2542-4653"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13328","checksum":"ffdb70b9ae7aa45ea4ea6096ecbd6431","success":1,"date_updated":"2023-07-31T08:44:38Z","file_size":1163444,"creator":"dernst","date_created":"2023-07-31T08:44:38Z","file_name":"2023_SciPostPhysics_Rammelmueller.pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 14","abstract":[{"text":"We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity \"breaks\" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2023-07-31T08:44:38Z","department":[{"_id":"MiLe"}],"date_updated":"2023-12-13T11:39:32Z","ddc":["530"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Physics and Astronomy"],"_id":"13278","doi":"10.21468/scipostphys.14.1.006","date_published":"2023-01-24T00:00:00Z","date_created":"2023-07-24T10:48:23Z","has_accepted_license":"1","isi":1,"year":"2023","day":"24","publication":"SciPost Physics","quality_controlled":"1","publisher":"SciPost Foundation","oa":1,"author":[{"last_name":"Rammelmüller","full_name":"Rammelmüller, Lukas","first_name":"Lukas"},{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"full_name":"Čufar, Matija","last_name":"Čufar","first_name":"Matija"},{"first_name":"Joachim","full_name":"Brand, Joachim","last_name":"Brand"},{"first_name":"Hans-Werner","full_name":"Hammer, Hans-Werner","last_name":"Hammer"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"article_processing_charge":"No","external_id":{"isi":["001000325800008"],"arxiv":["2204.01606"]},"title":"Magnetic impurity in a one-dimensional few-fermion system","citation":{"short":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, A. Volosniev, SciPost Physics 14 (2023).","ieee":"L. Rammelmüller, D. Huber, M. Čufar, J. Brand, H.-W. Hammer, and A. Volosniev, “Magnetic impurity in a one-dimensional few-fermion system,” SciPost Physics, vol. 14, no. 1. SciPost Foundation, 2023.","ama":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 2023;14(1). doi:10.21468/scipostphys.14.1.006","apa":"Rammelmüller, L., Huber, D., Čufar, M., Brand, J., Hammer, H.-W., & Volosniev, A. (2023). Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.14.1.006","mla":"Rammelmüller, Lukas, et al. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics, vol. 14, no. 1, 006, SciPost Foundation, 2023, doi:10.21468/scipostphys.14.1.006.","ista":"Rammelmüller L, Huber D, Čufar M, Brand J, Hammer H-W, Volosniev A. 2023. Magnetic impurity in a one-dimensional few-fermion system. SciPost Physics. 14(1), 006.","chicago":"Rammelmüller, Lukas, David Huber, Matija Čufar, Joachim Brand, Hans-Werner Hammer, and Artem Volosniev. “Magnetic Impurity in a One-Dimensional Few-Fermion System.” SciPost Physics. SciPost Foundation, 2023. https://doi.org/10.21468/scipostphys.14.1.006."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"006"},{"acknowledgement":"We thank Baofang Song as well as the developers of Channelflow for sharing their numerical codes, and Mukund Vasudevan and Holger Kantz for fruitful discussions. This work was supported by a grant from the Simons Foundation (662960, B. H.).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2023","day":"21","publication":"Physical Review Letters","date_published":"2023-07-21T00:00:00Z","doi":"10.1103/physrevlett.131.034002","date_created":"2023-07-24T09:43:59Z","article_number":"034002","project":[{"_id":"238598C6-32DE-11EA-91FC-C7463DDC885E","grant_number":"662960","name":"Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows"}],"citation":{"chicago":"Paranjape, Chaitanya S, Gökhan Yalniz, Yohann Duguet, Nazmi B Budanur, and Björn Hof. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/physrevlett.131.034002.","ista":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. 2023. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 131(3), 034002.","mla":"Paranjape, Chaitanya S., et al. “Direct Path from Turbulence to Time-Periodic Solutions.” Physical Review Letters, vol. 131, no. 3, 034002, American Physical Society, 2023, doi:10.1103/physrevlett.131.034002.","ama":"Paranjape CS, Yalniz G, Duguet Y, Budanur NB, Hof B. Direct path from turbulence to time-periodic solutions. Physical Review Letters. 2023;131(3). doi:10.1103/physrevlett.131.034002","apa":"Paranjape, C. S., Yalniz, G., Duguet, Y., Budanur, N. B., & Hof, B. (2023). Direct path from turbulence to time-periodic solutions. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.131.034002","short":"C.S. Paranjape, G. Yalniz, Y. Duguet, N.B. Budanur, B. Hof, Physical Review Letters 131 (2023).","ieee":"C. S. Paranjape, G. Yalniz, Y. Duguet, N. B. Budanur, and B. Hof, “Direct path from turbulence to time-periodic solutions,” Physical Review Letters, vol. 131, no. 3. American Physical Society, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Chaitanya S","id":"3D85B7C4-F248-11E8-B48F-1D18A9856A87","last_name":"Paranjape","full_name":"Paranjape, Chaitanya S"},{"last_name":"Yalniz","orcid":"0000-0002-8490-9312","full_name":"Yalniz, Gökhan","first_name":"Gökhan","id":"66E74FA2-D8BF-11E9-8249-8DE2E5697425"},{"first_name":"Yohann","last_name":"Duguet","full_name":"Duguet, Yohann"},{"last_name":"Budanur","orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"}],"article_processing_charge":"No","external_id":{"isi":["001052929900004"],"arxiv":["2306.05098"]},"title":"Direct path from turbulence to time-periodic solutions","abstract":[{"lang":"eng","text":"Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2306.05098"}],"month":"07","intvolume":" 131","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":131,"issue":"3","_id":"13274","article_type":"original","type":"journal_article","status":"public","keyword":["General Physics and Astronomy"],"date_updated":"2023-12-13T11:40:19Z","department":[{"_id":"GradSch"},{"_id":"BjHo"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:10.1126/science.adf5568.","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” Science, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 2023;380(6652):1357-1362. doi:10.1126/science.adf5568","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adf5568","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362."},"title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","article_processing_charge":"No","external_id":{"isi":["001106405600028"]},"author":[{"first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975"},{"first_name":"Hongtao","last_name":"Chen","full_name":"Chen, Hongtao"},{"first_name":"Lev","full_name":"Barinov, Lev","last_name":"Barinov"},{"last_name":"Zoller","full_name":"Zoller, Benjamin","first_name":"Benjamin"},{"first_name":"Thomas","full_name":"Gregor, Thomas","last_name":"Gregor"}],"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"publication":"Science","day":"29","year":"2023","isi":1,"date_created":"2023-07-23T22:01:12Z","date_published":"2023-06-29T00:00:00Z","doi":"10.1126/science.adf5568","page":"1357-1362","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","date_updated":"2023-12-13T11:41:07Z","department":[{"_id":"EdHa"}],"_id":"13261","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"issue":"6652","volume":380,"oa_version":"Preprint","abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}],"intvolume":" 380","month":"06","main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"scopus_import":"1"},{"article_processing_charge":"No","author":[{"first_name":"Maria","id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"department":[{"_id":"KrCh"}],"title":"kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games","date_updated":"2023-12-13T11:42:37Z","citation":{"mla":"Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.","apa":"Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564","ama":"Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564","short":"M. Kleshnina, (2023).","ieee":"M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.","chicago":"Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.","ista":"Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"type":"research_data_reference","status":"public","_id":"13336","date_created":"2023-07-31T11:30:46Z","doi":"10.5281/ZENODO.8059564","date_published":"2023-06-20T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","id":"13258","status":"public"}]},"year":"2023","day":"20","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8059564"}],"oa":1,"publisher":"Zenodo","month":"06","oa_version":"Published Version"},{"date_created":"2023-08-01T14:19:16Z","date_published":"2023-08-01T00:00:00Z","doi":"10.3847/1538-4357/acd118","year":"2023","isi":1,"has_accepted_license":"1","publication":"The Astrophysical Journal","day":"01","oa":1,"quality_controlled":"1","publisher":"American Astronomical Society","acknowledgement":"This paper includes data collected by the Kepler mission and obtained from the MAST data archive at the Space Telescope Science Institute (STScI). Funding for the Kepler mission is provided by the NASA Science Mission Directorate. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5–26555. We acknowledge that this research was supported in part by the National Science Foundation under grant No. NSF PHY-1748958. S.M. acknowledges support from the Spanish Ministry of Science and Innovation (MICINN) with the Ramón y Cajal fellowship No. RYC-2015-17697, the grant No. PID2019-107061GB-C66, and through AEI under the Severo Ochoa Centres of Excellence Programme 2020–2023 (CEX2019-000920-S). S.M. and D.G.R. acknowledge support from the Spanish Ministry of Science and Innovation (MICINN) with the grant No. PID2019-107187GB-I00. Z.R.C. acknowledges support from National Aeronautics and Space Administration via the TESS Guest Investigator Program (grant No. 80NSSC18K18584). The work presented here was partially supported by the NASA grant NNX17AF27G. A.R.G.S. acknowledges the support by FCT through national funds and by FEDER through COMPETE2020 by the following grants: UIDB/04434/2020 and UIDP/04434/2020. A.R.G.S. is supported by FCT through the work contract No. 2020.02480.CEECIND/CP1631/CT0001. R.A.G., L.A., and S.N.B. acknowledge the support from PLATO and GOLF CNES grants. S.N.B. acknowledges support from PLATO ASI-INAF agreement No. 2015-019-R.1-2018.","external_id":{"isi":["001034185700001"]},"article_processing_charge":"Yes","author":[{"full_name":"Mathur, Savita","last_name":"Mathur","first_name":"Savita"},{"last_name":"Claytor","full_name":"Claytor, Zachary R.","first_name":"Zachary R."},{"first_name":"Ângela R. G.","last_name":"Santos","full_name":"Santos, Ângela R. G."},{"last_name":"García","full_name":"García, Rafael A.","first_name":"Rafael A."},{"first_name":"Louis","last_name":"Amard","full_name":"Amard, Louis"},{"full_name":"Bugnet, Lisa Annabelle","orcid":"0000-0003-0142-4000","last_name":"Bugnet","id":"d9edb345-f866-11ec-9b37-d119b5234501","first_name":"Lisa Annabelle"},{"first_name":"Enrico","last_name":"Corsaro","full_name":"Corsaro, Enrico"},{"last_name":"Bonanno","full_name":"Bonanno, Alfio","first_name":"Alfio"},{"last_name":"Breton","full_name":"Breton, Sylvain N.","first_name":"Sylvain N."},{"first_name":"Diego","last_name":"Godoy-Rivera","full_name":"Godoy-Rivera, Diego"},{"full_name":"Pinsonneault, Marc H.","last_name":"Pinsonneault","first_name":"Marc H."},{"first_name":"Jennifer","full_name":"van Saders, Jennifer","last_name":"van Saders"}],"title":"Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations","citation":{"ista":"Mathur S, Claytor ZR, Santos ÂRG, García RA, Amard L, Bugnet LA, Corsaro E, Bonanno A, Breton SN, Godoy-Rivera D, Pinsonneault MH, van Saders J. 2023. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 952(2), 131.","chicago":"Mathur, Savita, Zachary R. Claytor, Ângela R. G. Santos, Rafael A. García, Louis Amard, Lisa Annabelle Bugnet, Enrico Corsaro, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal. American Astronomical Society, 2023. https://doi.org/10.3847/1538-4357/acd118.","ieee":"S. Mathur et al., “Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations,” The Astrophysical Journal, vol. 952, no. 2. American Astronomical Society, 2023.","short":"S. Mathur, Z.R. Claytor, Â.R.G. Santos, R.A. García, L. Amard, L.A. Bugnet, E. Corsaro, A. Bonanno, S.N. Breton, D. Godoy-Rivera, M.H. Pinsonneault, J. van Saders, The Astrophysical Journal 952 (2023).","ama":"Mathur S, Claytor ZR, Santos ÂRG, et al. Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. 2023;952(2). doi:10.3847/1538-4357/acd118","apa":"Mathur, S., Claytor, Z. R., Santos, Â. R. G., García, R. A., Amard, L., Bugnet, L. A., … van Saders, J. (2023). Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/acd118","mla":"Mathur, Savita, et al. “Magnetic Activity Evolution of Solar-like Stars. I. Sph–Age Relation Derived from Kepler Observations.” The Astrophysical Journal, vol. 952, no. 2, 131, American Astronomical Society, 2023, doi:10.3847/1538-4357/acd118."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"131","volume":952,"issue":"2","publication_status":"published","publication_identifier":{"eissn":["1538-4357"],"issn":["0004-637X"]},"language":[{"iso":"eng"}],"file":[{"file_size":4192386,"date_updated":"2023-08-02T07:42:26Z","creator":"dernst","file_name":"2023_AstrophysicalJour_Mathur.pdf","date_created":"2023-08-02T07:42:26Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"f12452834d7ed6748dbf5ace18af4723","file_id":"13448"}],"intvolume":" 952","month":"08","abstract":[{"text":"The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"LiBu"}],"file_date_updated":"2023-08-02T07:42:26Z","date_updated":"2023-12-13T12:00:15Z","ddc":["520"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"status":"public","_id":"13443"},{"oa":1,"quality_controlled":"1","publisher":"American Association for the Advancement of Science","acknowledgement":"Wethank Y.Iwayama, K.Ohtawa, K.Fukumoto,andN. Mataga (RIKENRRD) for technical assistance in Quartz-Seq2analyses; M. Mouri(RIKENCSRS)for technical support with plasmid construction and transactivation assay; Y. Ikeda (NAIST) for technical support with tissue culture; and A. Furuta for technical support in bulk RNA-seq analysis. We also thank the Single-cell Omics Laboratory for technical consultation in scRNA-seq analyses, the members of the Laboratory for Bioinformatics Research at the RIKEN Center for Biosystems Dynamics Research, and A. Matsushima and T. Ichikawa for IT infrastructure management. This work was supported by JSPS KAKENHI(17K15146,19H05670,20K06712,20H04894,20H05431,and 22H04713 to M.I. and 20H03284 and 20H05911 to K.S.), by the JST FOREST Program (JPMJFR214H to M.I.), by The Naito Foundation to M.I.; by Takeda Science Foundation to M.I,and by the Shiseido Female Researcher Science Grant to M.I. This work was partially supported by RIKENE pigenome Control Program, Medical Research Center Initiative for High Depth Omics, and JST CREST(JPMJCR16G3and JPMJCR1926)to I.N.","date_created":"2023-07-23T22:01:11Z","date_published":"2023-07-07T00:00:00Z","doi":"10.1126/sciadv.adg6983","page":"eadg6983","publication":"Science Advances","day":"07","year":"2023","isi":1,"has_accepted_license":"1","title":"WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus","article_processing_charge":"Yes","external_id":{"pmid":["37418524"],"isi":["001030983100012"]},"author":[{"full_name":"Ogura, Nao","last_name":"Ogura","first_name":"Nao"},{"last_name":"Sasagawa","full_name":"Sasagawa, Yohei","first_name":"Yohei"},{"first_name":"Tasuku","id":"d5a17a4a-e534-11eb-93ec-91fa2aa9bd57","full_name":"Ito, Tasuku","orcid":"0000-0002-2482-9089","last_name":"Ito"},{"full_name":"Tameshige, Toshiaki","last_name":"Tameshige","first_name":"Toshiaki"},{"first_name":"Satomi","last_name":"Kawai","full_name":"Kawai, Satomi"},{"full_name":"Sano, Masaki","last_name":"Sano","first_name":"Masaki"},{"first_name":"Yuki","last_name":"Doll","full_name":"Doll, Yuki"},{"last_name":"Iwase","full_name":"Iwase, Akira","first_name":"Akira"},{"first_name":"Ayako","full_name":"Kawamura, Ayako","last_name":"Kawamura"},{"first_name":"Takamasa","last_name":"Suzuki","full_name":"Suzuki, Takamasa"},{"first_name":"Itoshi","last_name":"Nikaido","full_name":"Nikaido, Itoshi"},{"first_name":"Keiko","last_name":"Sugimoto","full_name":"Sugimoto, Keiko"},{"full_name":"Ikeuchi, Momoko","last_name":"Ikeuchi","first_name":"Momoko"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Ogura, Nao, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances, vol. 9, no. 27, American Association for the Advancement of Science, 2023, p. eadg6983, doi:10.1126/sciadv.adg6983.","short":"N. Ogura, Y. Sasagawa, T. Ito, T. Tameshige, S. Kawai, M. Sano, Y. Doll, A. Iwase, A. Kawamura, T. Suzuki, I. Nikaido, K. Sugimoto, M. Ikeuchi, Science Advances 9 (2023) eadg6983.","ieee":"N. Ogura et al., “WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus,” Science Advances, vol. 9, no. 27. American Association for the Advancement of Science, p. eadg6983, 2023.","ama":"Ogura N, Sasagawa Y, Ito T, et al. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 2023;9(27):eadg6983. doi:10.1126/sciadv.adg6983","apa":"Ogura, N., Sasagawa, Y., Ito, T., Tameshige, T., Kawai, S., Sano, M., … Ikeuchi, M. (2023). WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg6983","chicago":"Ogura, Nao, Yohei Sasagawa, Tasuku Ito, Toshiaki Tameshige, Satomi Kawai, Masaki Sano, Yuki Doll, et al. “WUSCHEL-RELATED HOMEOBOX 13 Suppresses de Novo Shoot Regeneration via Cell Fate Control of Pluripotent Callus.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg6983.","ista":"Ogura N, Sasagawa Y, Ito T, Tameshige T, Kawai S, Sano M, Doll Y, Iwase A, Kawamura A, Suzuki T, Nikaido I, Sugimoto K, Ikeuchi M. 2023. WUSCHEL-RELATED HOMEOBOX 13 suppresses de novo shoot regeneration via cell fate control of pluripotent callus. Science Advances. 9(27), eadg6983."},"intvolume":" 9","month":"07","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Plants can regenerate their bodies via de novo establishment of shoot apical meristems (SAMs) from pluripotent callus. Only a small fraction of callus cells is eventually specified into SAMs but the molecular mechanisms underlying fate specification remain obscure. The expression of WUSCHEL (WUS) is an early hallmark of SAM fate acquisition. Here, we show that a WUS paralog, WUSCHEL-RELATED HOMEOBOX 13 (WOX13), negatively regulates SAM formation from callus in Arabidopsis thaliana. WOX13 promotes non-meristematic cell fate via transcriptional repression of WUS and other SAM regulators and activation of cell wall modifiers. Our Quartz-Seq2–based single cell transcriptome revealed that WOX13 plays key roles in determining cellular identity of callus cell population. We propose that reciprocal inhibition between WUS and WOX13 mediates critical cell fate determination in pluripotent cell population, which has a major impact on regeneration efficiency."}],"issue":"27","volume":9,"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"13338","checksum":"f59217e1083767777318b5d0cc5e141d","creator":"dernst","file_size":1759993,"date_updated":"2023-08-01T06:40:35Z","file_name":"2023_ScienceAdvance_Ogura.pdf","date_created":"2023-08-01T06:40:35Z"}],"publication_status":"published","publication_identifier":{"eissn":["2375-2548"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"13259","file_date_updated":"2023-08-01T06:40:35Z","ddc":["580"],"date_updated":"2023-12-13T11:59:29Z"},{"isi":1,"year":"2023","day":"27","publication":"GigaScience","date_published":"2023-07-27T00:00:00Z","doi":"10.1093/gigascience/giad045","date_created":"2023-08-06T22:01:13Z","acknowledgement":"Our article is dedicated to all freedom-loving people around the world and to the people of Ukraine who fight for our freedom. Special thanks to Anita Bandrowski, Oleksandra V. Ivashchenko, and Sanita Reinsone for the helpful review, valuable criticism, and useful suggestions while preparing this manuscript, and to Tetiana Yes'kova for helping with Ukrainian translation.\r\nAll authors volunteered their time. No funding supported work on this article.","quality_controlled":"1","publisher":"Oxford Academic","oa":1,"citation":{"mla":"Wolfsberger, Walter, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience, vol. 12, Oxford Academic, 2023, doi:10.1093/gigascience/giad045.","short":"W. Wolfsberger, K. Chhugani, K. Shchubelka, A. Frolova, Y. Salyha, O. Zlenko, M. Arych, D. Dziuba, A. Parkhomenko, V. Smolanka, Z.H. Gümüş, E. Sezgin, A. Diaz-Lameiro, V.R. Toth, M. Maci, E. Bortz, F. Kondrashov, P.M. Morton, P.P. Łabaj, V. Romero, J. Hlávka, S. Mangul, T.K. Oleksyk, GigaScience 12 (2023).","ieee":"W. Wolfsberger et al., “Scientists without borders: Lessons from Ukraine,” GigaScience, vol. 12. Oxford Academic, 2023.","apa":"Wolfsberger, W., Chhugani, K., Shchubelka, K., Frolova, A., Salyha, Y., Zlenko, O., … Oleksyk, T. K. (2023). Scientists without borders: Lessons from Ukraine. GigaScience. Oxford Academic. https://doi.org/10.1093/gigascience/giad045","ama":"Wolfsberger W, Chhugani K, Shchubelka K, et al. Scientists without borders: Lessons from Ukraine. GigaScience. 2023;12. doi:10.1093/gigascience/giad045","chicago":"Wolfsberger, Walter, Karishma Chhugani, Khrystyna Shchubelka, Alina Frolova, Yuriy Salyha, Oksana Zlenko, Mykhailo Arych, et al. “Scientists without Borders: Lessons from Ukraine.” GigaScience. Oxford Academic, 2023. https://doi.org/10.1093/gigascience/giad045.","ista":"Wolfsberger W, Chhugani K, Shchubelka K, Frolova A, Salyha Y, Zlenko O, Arych M, Dziuba D, Parkhomenko A, Smolanka V, Gümüş ZH, Sezgin E, Diaz-Lameiro A, Toth VR, Maci M, Bortz E, Kondrashov F, Morton PM, Łabaj PP, Romero V, Hlávka J, Mangul S, Oleksyk TK. 2023. Scientists without borders: Lessons from Ukraine. GigaScience. 12."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Walter","full_name":"Wolfsberger, Walter","last_name":"Wolfsberger"},{"first_name":"Karishma","full_name":"Chhugani, Karishma","last_name":"Chhugani"},{"last_name":"Shchubelka","full_name":"Shchubelka, Khrystyna","first_name":"Khrystyna"},{"last_name":"Frolova","full_name":"Frolova, Alina","first_name":"Alina"},{"first_name":"Yuriy","full_name":"Salyha, Yuriy","last_name":"Salyha"},{"last_name":"Zlenko","full_name":"Zlenko, Oksana","first_name":"Oksana"},{"full_name":"Arych, Mykhailo","last_name":"Arych","first_name":"Mykhailo"},{"first_name":"Dmytro","full_name":"Dziuba, Dmytro","last_name":"Dziuba"},{"first_name":"Andrii","full_name":"Parkhomenko, Andrii","last_name":"Parkhomenko"},{"full_name":"Smolanka, Volodymyr","last_name":"Smolanka","first_name":"Volodymyr"},{"first_name":"Zeynep H.","last_name":"Gümüş","full_name":"Gümüş, Zeynep H."},{"full_name":"Sezgin, Efe","last_name":"Sezgin","first_name":"Efe"},{"first_name":"Alondra","last_name":"Diaz-Lameiro","full_name":"Diaz-Lameiro, Alondra"},{"full_name":"Toth, Viktor R.","last_name":"Toth","first_name":"Viktor R."},{"first_name":"Megi","full_name":"Maci, Megi","last_name":"Maci"},{"full_name":"Bortz, Eric","last_name":"Bortz","first_name":"Eric"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Patricia M.","last_name":"Morton","full_name":"Morton, Patricia M."},{"first_name":"Paweł P.","last_name":"Łabaj","full_name":"Łabaj, Paweł P."},{"full_name":"Romero, Veronika","last_name":"Romero","first_name":"Veronika"},{"last_name":"Hlávka","full_name":"Hlávka, Jakub","first_name":"Jakub"},{"first_name":"Serghei","full_name":"Mangul, Serghei","last_name":"Mangul"},{"last_name":"Oleksyk","full_name":"Oleksyk, Taras K.","first_name":"Taras K."}],"external_id":{"pmid":["37496156"],"isi":["001081086100001"]},"article_processing_charge":"Yes","title":"Scientists without borders: Lessons from Ukraine","publication_identifier":{"eissn":["2047-217X"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"volume":12,"abstract":[{"text":"Conflicts and natural disasters affect entire populations of the countries involved and, in addition to the thousands of lives destroyed, have a substantial negative impact on the scientific advances these countries provide. The unprovoked invasion of Ukraine by Russia, the devastating earthquake in Turkey and Syria, and the ongoing conflicts in the Middle East are just a few examples. Millions of people have been killed or displaced, their futures uncertain. These events have resulted in extensive infrastructure collapse, with loss of electricity, transportation, and access to services. Schools, universities, and research centers have been destroyed along with decades’ worth of data, samples, and findings. Scholars in disaster areas face short- and long-term problems in terms of what they can accomplish now for obtaining grants and for employment in the long run. In our interconnected world, conflicts and disasters are no longer a local problem but have wide-ranging impacts on the entire world, both now and in the future. Here, we focus on the current and ongoing impact of war on the scientific community within Ukraine and from this draw lessons that can be applied to all affected countries where scientists at risk are facing hardship. We present and classify examples of effective and feasible mechanisms used to support researchers in countries facing hardship and discuss how these can be implemented with help from the international scientific community and what more is desperately needed. Reaching out, providing accessible training opportunities, and developing collaborations should increase inclusion and connectivity, support scientific advancements within affected communities, and expedite postwar and disaster recovery.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/gigascience/giad045"}],"month":"07","intvolume":" 12","date_updated":"2023-12-13T12:01:46Z","department":[{"_id":"FyKo"}],"_id":"13976","type":"journal_article","article_type":"original","status":"public"},{"department":[{"_id":"TiBr"}],"file_date_updated":"2023-08-07T07:19:42Z","date_updated":"2023-12-13T12:03:04Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","image":"/image/cc_by_nd.png","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","short":"CC BY-ND (4.0)"},"status":"public","_id":"13973","volume":73,"issue":"2","ec_funded":1,"license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_identifier":{"issn":["0373-0956"]},"publication_status":"published","file":[{"creator":"dernst","date_updated":"2023-08-07T07:19:42Z","file_size":1529821,"date_created":"2023-08-07T07:19:42Z","file_name":"2023_AnnalesFourier_Lyczak.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"daf53fc614c894422e4c0fb3d2a2ae3e","file_id":"13977","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"05","intvolume":" 73","abstract":[{"lang":"eng","text":"We construct families of log K3 surfaces and study the arithmetic of their members. We use this to produce explicit surfaces with an order 5 Brauer–Manin obstruction to the integral Hasse principle."}],"oa_version":"Published Version","author":[{"first_name":"Julian","id":"3572849A-F248-11E8-B48F-1D18A9856A87","full_name":"Lyczak, Julian","last_name":"Lyczak"}],"external_id":{"isi":["001000279500001"],"arxiv":["2005.14013"]},"article_processing_charge":"Yes (in subscription journal)","title":"Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces","citation":{"chicago":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier, 2023. https://doi.org/10.5802/aif.3529.","ista":"Lyczak J. 2023. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 73(2), 447–478.","mla":"Lyczak, Julian. “Order 5 Brauer–Manin Obstructions to the Integral Hasse Principle on Log K3 Surfaces.” Annales de l’Institut Fourier, vol. 73, no. 2, Association des Annales de l’Institut Fourier, 2023, pp. 447–78, doi:10.5802/aif.3529.","ieee":"J. Lyczak, “Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces,” Annales de l’Institut Fourier, vol. 73, no. 2. Association des Annales de l’Institut Fourier, pp. 447–478, 2023.","short":"J. Lyczak, Annales de l’Institut Fourier 73 (2023) 447–478.","apa":"Lyczak, J. (2023). Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. Association des Annales de l’Institut Fourier. https://doi.org/10.5802/aif.3529","ama":"Lyczak J. Order 5 Brauer–Manin obstructions to the integral Hasse principle on log K3 surfaces. Annales de l’Institut Fourier. 2023;73(2):447-478. doi:10.5802/aif.3529"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"page":"447-478","doi":"10.5802/aif.3529","date_published":"2023-05-12T00:00:00Z","date_created":"2023-08-06T22:01:12Z","isi":1,"has_accepted_license":"1","year":"2023","day":"12","publication":"Annales de l'Institut Fourier","publisher":"Association des Annales de l'Institut Fourier","quality_controlled":"1","oa":1,"acknowledgement":"This paper was completed as part of a project which received funding from the\r\nEuropean Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie grant agreement No. 754411."},{"type":"journal_article","article_type":"original","status":"public","_id":"13974","department":[{"_id":"UlWa"}],"date_updated":"2023-12-13T12:03:35Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1812.04911","open_access":"1"}],"scopus_import":"1","month":"07","abstract":[{"text":"The Tverberg theorem is one of the cornerstones of discrete geometry. It states that, given a set X of at least (d+1)(r−1)+1 points in Rd, one can find a partition X=X1∪⋯∪Xr of X, such that the convex hulls of the Xi, i=1,…,r, all share a common point. In this paper, we prove a trengthening of this theorem that guarantees a partition which, in addition to the above, has the property that the boundaries of full-dimensional convex hulls have pairwise nonempty intersections. Possible generalizations and algorithmic aspects are also discussed. As a concrete application, we show that any n points in the plane in general position span ⌊n/3⌋ vertex-disjoint triangles that are pairwise crossing, meaning that their boundaries have pairwise nonempty intersections; this number is clearly best possible. A previous result of Álvarez-Rebollar et al. guarantees ⌊n/6⌋pairwise crossing triangles. Our result generalizes to a result about simplices in Rd, d≥2.","lang":"eng"}],"oa_version":"Preprint","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6647"}]},"publication_status":"epub_ahead","publication_identifier":{"issn":["0179-5376"],"eissn":["1432-0444"]},"language":[{"iso":"eng"}],"project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","external_id":{"isi":["001038546500001"],"arxiv":["1812.04911"]},"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek"},{"first_name":"Bernd","last_name":"Gärtner","full_name":"Gärtner, Bernd"},{"first_name":"Andrey","last_name":"Kupavskii","full_name":"Kupavskii, Andrey"},{"first_name":"Pavel","full_name":"Valtr, Pavel","last_name":"Valtr"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"title":"The crossing Tverberg theorem","citation":{"chicago":"Fulek, Radoslav, Bernd Gärtner, Andrey Kupavskii, Pavel Valtr, and Uli Wagner. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00532-x.","ista":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. 2023. The crossing Tverberg theorem. Discrete and Computational Geometry.","mla":"Fulek, Radoslav, et al. “The Crossing Tverberg Theorem.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00532-x.","ama":"Fulek R, Gärtner B, Kupavskii A, Valtr P, Wagner U. The crossing Tverberg theorem. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00532-x","apa":"Fulek, R., Gärtner, B., Kupavskii, A., Valtr, P., & Wagner, U. (2023). The crossing Tverberg theorem. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00532-x","short":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, U. Wagner, Discrete and Computational Geometry (2023).","ieee":"R. Fulek, B. Gärtner, A. Kupavskii, P. Valtr, and U. Wagner, “The crossing Tverberg theorem,” Discrete and Computational Geometry. Springer Nature, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"Part of the research leading to this paper was done during the 16th Gremo Workshop on Open Problems (GWOP), Waltensburg, Switzerland, June 12–16, 2018. We thank Patrick Schnider for suggesting the problem, and Stefan Felsner, Malte Milatz, and Emo Welzl for fruitful discussions during the workshop. We also thank Stefan Felsner and Manfred Scheucher for finding, communicating the example from Sect. 3.3, and the kind permission to include their visualization of the point set. We thank Dömötör Pálvölgyi, the SoCG reviewers, and DCG reviewers for various helpful comments.\r\nR. Fulek gratefully acknowledges support from Austrian Science Fund (FWF), Project M2281-N35. A. Kupavskii was supported by the Advanced Postdoc.Mobility Grant no. P300P2_177839 of the Swiss National Science Foundation. Research by P. Valtr was supported by the Grant no. 18-19158 S of the Czech Science Foundation (GAČR).","date_created":"2023-08-06T22:01:12Z","doi":"10.1007/s00454-023-00532-x","date_published":"2023-07-27T00:00:00Z","year":"2023","isi":1,"publication":"Discrete and Computational Geometry","day":"27"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Campbell AJ, O’Rourke S. 2023. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability.","chicago":"Campbell, Andrew J, and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability. Springer Nature, 2023. https://doi.org/10.1007/s10959-023-01275-4.","ieee":"A. J. Campbell and S. O’Rourke, “Spectrum of Lévy–Khintchine random laplacian matrices,” Journal of Theoretical Probability. Springer Nature, 2023.","short":"A.J. Campbell, S. O’Rourke, Journal of Theoretical Probability (2023).","apa":"Campbell, A. J., & O’Rourke, S. (2023). Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. Springer Nature. https://doi.org/10.1007/s10959-023-01275-4","ama":"Campbell AJ, O’Rourke S. Spectrum of Lévy–Khintchine random laplacian matrices. Journal of Theoretical Probability. 2023. doi:10.1007/s10959-023-01275-4","mla":"Campbell, Andrew J., and Sean O’Rourke. “Spectrum of Lévy–Khintchine Random Laplacian Matrices.” Journal of Theoretical Probability, Springer Nature, 2023, doi:10.1007/s10959-023-01275-4."},"title":"Spectrum of Lévy–Khintchine random laplacian matrices","author":[{"full_name":"Campbell, Andrew J","last_name":"Campbell","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4","first_name":"Andrew J"},{"last_name":"O’Rourke","full_name":"O’Rourke, Sean","first_name":"Sean"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001038341000001"],"arxiv":["2210.07927"]},"day":"26","publication":"Journal of Theoretical Probability","has_accepted_license":"1","isi":1,"year":"2023","doi":"10.1007/s10959-023-01275-4","date_published":"2023-07-26T00:00:00Z","date_created":"2023-08-06T22:01:13Z","acknowledgement":"The first author thanks Yizhe Zhu for pointing out reference [30]. We thank David Renfrew for comments on an earlier draft. We thank the anonymous referee for a careful reading and helpful comments.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"ddc":["510"],"date_updated":"2023-12-13T12:00:50Z","department":[{"_id":"LaEr"}],"_id":"13975","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1572-9230"],"issn":["0894-9840"]},"publication_status":"epub_ahead","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We consider the spectrum of random Laplacian matrices of the form Ln=An−Dn where An\r\n is a real symmetric random matrix and Dn is a diagonal matrix whose entries are equal to the corresponding row sums of An. If An is a Wigner matrix with entries in the domain of attraction of a Gaussian distribution, the empirical spectral measure of Ln is known to converge to the free convolution of a semicircle distribution and a standard real Gaussian distribution. We consider real symmetric random matrices An with independent entries (up to symmetry) whose row sums converge to a purely non-Gaussian infinitely divisible distribution, which fall into the class of Lévy–Khintchine random matrices first introduced by Jung [Trans Am Math Soc, 370, (2018)]. Our main result shows that the empirical spectral measure of Ln converges almost surely to a deterministic limit. A key step in the proof is to use the purely non-Gaussian nature of the row sums to build a random operator to which Ln converges in an appropriate sense. This operator leads to a recursive distributional equation uniquely describing the Stieltjes transform of the limiting empirical spectral measure."}],"month":"07","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10959-023-01275-4","open_access":"1"}]},{"issue":"3","volume":108,"publication_status":"published","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.10038","open_access":"1"}],"scopus_import":"1","intvolume":" 108","month":"07","abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KiMo"}],"date_updated":"2023-12-13T11:58:57Z","type":"journal_article","article_type":"original","status":"public","_id":"13257","date_created":"2023-07-23T22:01:10Z","doi":"10.1103/PhysRevB.108.035111","date_published":"2023-07-15T00:00:00Z","year":"2023","isi":1,"publication":"Physical Review B","day":"15","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","external_id":{"arxiv":["2208.10038"],"isi":["001062708600002"]},"article_processing_charge":"No","author":[{"last_name":"Shekhter","full_name":"Shekhter, A.","first_name":"A."},{"last_name":"Mcdonald","full_name":"Mcdonald, R. D.","first_name":"R. D."},{"first_name":"B. J.","full_name":"Ramshaw, B. J.","last_name":"Ramshaw"},{"last_name":"Modic","orcid":"0000-0001-9760-3147","full_name":"Modic, Kimberly A","first_name":"Kimberly A","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425"}],"title":"Magnetotropic susceptibility","citation":{"ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. Physical Review B. 2023;108(3). doi:10.1103/PhysRevB.108.035111","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., & Modic, K. A. (2023). Magnetotropic susceptibility. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.035111","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” Physical Review B, vol. 108, no. 3. American Physical Society, 2023.","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” Physical Review B, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:10.1103/PhysRevB.108.035111.","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.035111."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"035111"},{"_id":"13972","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2023-12-13T12:02:26Z","department":[{"_id":"BaPi"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"This Special Collection is dedicated to the field of photocatalytic synthesis and contains a diverse selection of original research contributions. It includes studies on catalyst development, mechanistic investigations, method development and the use of enabling technologies, illustrating the many facets of state-of-the-art research in photocatalytic synthesis. Further, emerging topics are surveyed and discussed in three reviews and a concept article."}],"month":"07","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/cctc.202300683"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1867-3899"],"issn":["1867-3880"]},"publication_status":"epub_ahead","article_number":"e202300683","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Næsborg, Line, et al. “Special Collection: Photocatalytic Synthesis.” ChemCatChem, e202300683, Wiley, 2023, doi:10.1002/cctc.202300683.","ieee":"L. Næsborg, B. Pieber, and O. S. Wenger, “Special Collection: Photocatalytic synthesis,” ChemCatChem. Wiley, 2023.","short":"L. Næsborg, B. Pieber, O.S. Wenger, ChemCatChem (2023).","apa":"Næsborg, L., Pieber, B., & Wenger, O. S. (2023). Special Collection: Photocatalytic synthesis. ChemCatChem. Wiley. https://doi.org/10.1002/cctc.202300683","ama":"Næsborg L, Pieber B, Wenger OS. Special Collection: Photocatalytic synthesis. ChemCatChem. 2023. doi:10.1002/cctc.202300683","chicago":"Næsborg, Line, Bartholomäus Pieber, and Oliver S. Wenger. “Special Collection: Photocatalytic Synthesis.” ChemCatChem. Wiley, 2023. https://doi.org/10.1002/cctc.202300683.","ista":"Næsborg L, Pieber B, Wenger OS. 2023. Special Collection: Photocatalytic synthesis. ChemCatChem., e202300683."},"title":"Special Collection: Photocatalytic synthesis","author":[{"full_name":"Næsborg, Line","last_name":"Næsborg","first_name":"Line"},{"last_name":"Pieber","full_name":"Pieber, Bartholomäus","orcid":"0000-0001-8689-388X","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus"},{"first_name":"Oliver S.","last_name":"Wenger","full_name":"Wenger, Oliver S."}],"article_processing_charge":"No","external_id":{"isi":["001037859900001"]},"publisher":"Wiley","quality_controlled":"1","oa":1,"day":"27","publication":"ChemCatChem","isi":1,"year":"2023","date_published":"2023-07-27T00:00:00Z","doi":"10.1002/cctc.202300683","date_created":"2023-08-06T22:01:12Z"},{"doi":"10.3389/fphy.2023.1202132","date_published":"2023-07-14T00:00:00Z","date_created":"2023-08-06T22:01:11Z","isi":1,"has_accepted_license":"1","year":"2023","day":"14","publication":"Frontiers in Physics","publisher":"Frontiers","quality_controlled":"1","oa":1,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863–BORGES. We further thank the office of the Federal Government of Lower Austria, K3-Group–Culture, Science and Education, for their financial support as part of the project “Responsive Wound Dressing”. We gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 888067).\r\nWe thank the Electron Microscopy Facility at IST Austria for their support with sputter coating the FO tips and Bernhard Pichler from AIT for software development to facilitate data evaluation.","author":[{"last_name":"Hasler","full_name":"Hasler, Roger","first_name":"Roger"},{"last_name":"Steger-Polt","full_name":"Steger-Polt, Marie Helene","first_name":"Marie Helene"},{"first_name":"Ciril","full_name":"Reiner-Rozman, Ciril","last_name":"Reiner-Rozman"},{"last_name":"Fossati","full_name":"Fossati, Stefan","first_name":"Stefan"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","last_name":"Lee","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598"},{"first_name":"Patrik","last_name":"Aspermair","full_name":"Aspermair, Patrik"},{"full_name":"Kleber, Christoph","last_name":"Kleber","first_name":"Christoph"},{"last_name":"Ibáñez","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria"},{"first_name":"Jakub","last_name":"Dostalek","full_name":"Dostalek, Jakub"},{"first_name":"Wolfgang","full_name":"Knoll, Wolfgang","last_name":"Knoll"}],"article_processing_charge":"Yes","external_id":{"isi":["001038636400001"]},"title":"Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing","citation":{"ista":"Hasler R, Steger-Polt MH, Reiner-Rozman C, Fossati S, Lee S, Aspermair P, Kleber C, Ibáñez M, Dostalek J, Knoll W. 2023. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 11, 1202132.","chicago":"Hasler, Roger, Marie Helene Steger-Polt, Ciril Reiner-Rozman, Stefan Fossati, Seungho Lee, Patrik Aspermair, Christoph Kleber, Maria Ibáñez, Jakub Dostalek, and Wolfgang Knoll. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics. Frontiers, 2023. https://doi.org/10.3389/fphy.2023.1202132.","short":"R. Hasler, M.H. Steger-Polt, C. Reiner-Rozman, S. Fossati, S. Lee, P. Aspermair, C. Kleber, M. Ibáñez, J. Dostalek, W. Knoll, Frontiers in Physics 11 (2023).","ieee":"R. Hasler et al., “Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing,” Frontiers in Physics, vol. 11. Frontiers, 2023.","ama":"Hasler R, Steger-Polt MH, Reiner-Rozman C, et al. Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. 2023;11. doi:10.3389/fphy.2023.1202132","apa":"Hasler, R., Steger-Polt, M. H., Reiner-Rozman, C., Fossati, S., Lee, S., Aspermair, P., … Knoll, W. (2023). Optical and electronic signal stabilization of plasmonic fiber optic gate electrodes: Towards improved real-time dual-mode biosensing. Frontiers in Physics. Frontiers. https://doi.org/10.3389/fphy.2023.1202132","mla":"Hasler, Roger, et al. “Optical and Electronic Signal Stabilization of Plasmonic Fiber Optic Gate Electrodes: Towards Improved Real-Time Dual-Mode Biosensing.” Frontiers in Physics, vol. 11, 1202132, Frontiers, 2023, doi:10.3389/fphy.2023.1202132."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"1202132","volume":11,"publication_identifier":{"eissn":["2296-424X"]},"publication_status":"published","file":[{"checksum":"fb36dda665e57bab006a000bf0faacd5","file_id":"13978","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-08-07T07:48:11Z","file_name":"2023_FrontiersPhysics_Hasler.pdf","date_updated":"2023-08-07T07:48:11Z","file_size":2421758,"creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 11","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"The use of multimodal readout mechanisms next to label-free real-time monitoring of biomolecular interactions can provide valuable insight into surface-based reaction mechanisms. To this end, the combination of an electrolyte-gated field-effect transistor (EG-FET) with a fiber optic-coupled surface plasmon resonance (FO-SPR) probe serving as gate electrode has been investigated to deconvolute surface mass and charge density variations associated to surface reactions. However, applying an electrochemical potential on such gold-coated FO-SPR gate electrodes can induce gradual morphological changes of the thin gold film, leading to an irreversible blue-shift of the SPR wavelength and a substantial signal drift. We show that mild annealing leads to optical and electronic signal stabilization (20-fold lower signal drift than as-sputtered fiber optic gates) and improved overall analytical performance characteristics. The thermal treatment prevents morphological changes of the thin gold-film occurring during operation, hence providing reliable and stable data immediately upon gate voltage application. Thus, the readout output of both transducing principles, the optical FO-SPR and electronic EG-FET, stays constant throughout the whole sensing time-window and the long-term effect of thermal treatment is also improved, providing stable signals even after 1 year of storage. Annealing should therefore be considered a necessary modification for applying fiber optic gate electrodes in real-time multimodal investigations of surface reactions at the solid-liquid interface.","lang":"eng"}],"oa_version":"Published Version","file_date_updated":"2023-08-07T07:48:11Z","department":[{"_id":"MaIb"}],"date_updated":"2023-12-13T12:04:10Z","ddc":["530"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"13968"},{"acknowledgement":"M. Bulíček and J. Málek acknowledge the support of the project No. 20-11027X financed by the Czech Science foundation (GAČR). M. Bulíček and J. Málek are members of the Nečas Center for Mathematical Modelling.\r\nOpen access publishing supported by the National Technical Library in Prague.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Journal of Mathematical Fluid Mechanics","day":"01","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-08-13T22:01:13Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1007/s00021-023-00803-w","article_number":"72","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bulíček M, Málek J, Maringová E. 2023. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 25(3), 72.","chicago":"Bulíček, Miroslav, Josef Málek, and Erika Maringová. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics. Springer Nature, 2023. https://doi.org/10.1007/s00021-023-00803-w.","ieee":"M. Bulíček, J. Málek, and E. Maringová, “On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary,” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3. Springer Nature, 2023.","short":"M. Bulíček, J. Málek, E. Maringová, Journal of Mathematical Fluid Mechanics 25 (2023).","apa":"Bulíček, M., Málek, J., & Maringová, E. (2023). On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. Springer Nature. https://doi.org/10.1007/s00021-023-00803-w","ama":"Bulíček M, Málek J, Maringová E. On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary. Journal of Mathematical Fluid Mechanics. 2023;25(3). doi:10.1007/s00021-023-00803-w","mla":"Bulíček, Miroslav, et al. “On Unsteady Internal Flows of Incompressible Fluids Characterized by Implicit Constitutive Equations in the Bulk and on the Boundary.” Journal of Mathematical Fluid Mechanics, vol. 25, no. 3, 72, Springer Nature, 2023, doi:10.1007/s00021-023-00803-w."},"title":"On unsteady internal flows of incompressible fluids characterized by implicit constitutive equations in the bulk and on the boundary","external_id":{"arxiv":["2301.12834"],"isi":["001040354900001"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Bulíček, Miroslav","last_name":"Bulíček","first_name":"Miroslav"},{"first_name":"Josef","full_name":"Málek, Josef","last_name":"Málek"},{"last_name":"Maringová","full_name":"Maringová, Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","first_name":"Erika"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Long-time and large-data existence of weak solutions for initial- and boundary-value problems concerning three-dimensional flows of incompressible fluids is nowadays available not only for Navier–Stokes fluids but also for various fluid models where the relation between the Cauchy stress tensor and the symmetric part of the velocity gradient is nonlinear. The majority of such studies however concerns models where such a dependence is explicit (the stress is a function of the velocity gradient), which makes the class of studied models unduly restrictive. The same concerns boundary conditions, or more precisely the slipping mechanisms on the boundary, where the no-slip is still the most preferred condition considered in the literature. Our main objective is to develop a robust mathematical theory for unsteady internal flows of implicitly constituted incompressible fluids with implicit relations between the tangential projections of the velocity and the normal traction on the boundary. The theory covers numerous rheological models used in chemistry, biorheology, polymer and food industry as well as in geomechanics. It also includes, as special cases, nonlinear slip as well as stick–slip boundary conditions. Unlike earlier studies, the conditions characterizing admissible classes of constitutive equations are expressed by means of tools of elementary calculus. In addition, a fully constructive proof (approximation scheme) is incorporated. Finally, we focus on the question of uniqueness of such weak solutions."}],"intvolume":" 25","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"date_updated":"2023-08-14T07:24:17Z","file_size":845748,"creator":"dernst","date_created":"2023-08-14T07:24:17Z","file_name":"2023_JourMathFluidMech_Bulicek.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14046","checksum":"c549cd8f0dd02ed60477a05ca045f481","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1422-6952"],"issn":["1422-6928"]},"issue":"3","volume":25,"_id":"14042","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["510"],"date_updated":"2023-12-13T12:08:08Z","file_date_updated":"2023-08-14T07:24:17Z","department":[{"_id":"JuFi"}]},{"title":"3D cell segregation geometry and dynamics are governed by tissue surface tension regulation","article_processing_charge":"Yes","external_id":{"pmid":["37542157"],"isi":["001042544100001"]},"author":[{"full_name":"Méhes, Elod","last_name":"Méhes","first_name":"Elod"},{"first_name":"Enys","last_name":"Mones","full_name":"Mones, Enys"},{"last_name":"Varga","full_name":"Varga, Máté","first_name":"Máté"},{"full_name":"Zsigmond, Áron","last_name":"Zsigmond","first_name":"Áron"},{"full_name":"Biri-Kovács, Beáta","last_name":"Biri-Kovács","first_name":"Beáta"},{"last_name":"Nyitray","full_name":"Nyitray, László","first_name":"László"},{"first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","orcid":"0000-0003-2676-3367","full_name":"Barone, Vanessa"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4761-5996","full_name":"Krens, Gabriel","last_name":"Krens"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J"},{"first_name":"Tamás","last_name":"Vicsek","full_name":"Vicsek, Tamás"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Méhes, Elod, et al. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology, vol. 6, 817, Springer Nature, 2023, doi:10.1038/s42003-023-05181-7.","ieee":"E. Méhes et al., “3D cell segregation geometry and dynamics are governed by tissue surface tension regulation,” Communications Biology, vol. 6. Springer Nature, 2023.","short":"E. Méhes, E. Mones, M. Varga, Á. Zsigmond, B. Biri-Kovács, L. Nyitray, V. Barone, G. Krens, C.-P.J. Heisenberg, T. Vicsek, Communications Biology 6 (2023).","apa":"Méhes, E., Mones, E., Varga, M., Zsigmond, Á., Biri-Kovács, B., Nyitray, L., … Vicsek, T. (2023). 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-023-05181-7","ama":"Méhes E, Mones E, Varga M, et al. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 2023;6. doi:10.1038/s42003-023-05181-7","chicago":"Méhes, Elod, Enys Mones, Máté Varga, Áron Zsigmond, Beáta Biri-Kovács, László Nyitray, Vanessa Barone, Gabriel Krens, Carl-Philipp J Heisenberg, and Tamás Vicsek. “3D Cell Segregation Geometry and Dynamics Are Governed by Tissue Surface Tension Regulation.” Communications Biology. Springer Nature, 2023. https://doi.org/10.1038/s42003-023-05181-7.","ista":"Méhes E, Mones E, Varga M, Zsigmond Á, Biri-Kovács B, Nyitray L, Barone V, Krens G, Heisenberg C-PJ, Vicsek T. 2023. 3D cell segregation geometry and dynamics are governed by tissue surface tension regulation. Communications Biology. 6, 817."},"article_number":"817","date_created":"2023-08-13T22:01:13Z","date_published":"2023-08-04T00:00:00Z","doi":"10.1038/s42003-023-05181-7","publication":"Communications Biology","day":"04","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"quality_controlled":"1","publisher":"Springer Nature","acknowledgement":"We thank Marton Gulyas (ELTE Eötvös University) for development of videomicroscopy experiment manager and image analysis software. Authors are grateful to Gabor Forgacs (University of Missouri) for critical reading of earlier versions of this manuscript as well as to Zsuzsa Akos and Andras Czirok (ELTE Eötvös University) for fruitful discussions. This work was supported by EU FP7, ERC COLLMOT Project No 227878 to TV, the National Research Development and Innovation Fund of Hungary, K119359 and also Project No 2018-1.2.1-NKP-2018-00005 to LN. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 955576. MV was supported by the Ja´nos Bolyai Fellowship of the Hungarian Academy of Sciences.\r\nOpen access funding provided by Eötvös Loránd University.","file_date_updated":"2023-08-14T07:17:36Z","department":[{"_id":"CaHe"},{"_id":"Bio"}],"ddc":["570"],"date_updated":"2023-12-13T12:07:33Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14041","volume":6,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14045","checksum":"1f9324f736bdbb76426b07736651c4cd","file_size":10181997,"date_updated":"2023-08-14T07:17:36Z","creator":"dernst","file_name":"2023_CommBiology_Mehes.pdf","date_created":"2023-08-14T07:17:36Z"}],"publication_status":"published","publication_identifier":{"eissn":["2399-3642"]},"intvolume":" 6","month":"08","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Tissue morphogenesis and patterning during development involve the segregation of cell types. Segregation is driven by differential tissue surface tensions generated by cell types through controlling cell-cell contact formation by regulating adhesion and actomyosin contractility-based cellular cortical tensions. We use vertebrate tissue cell types and zebrafish germ layer progenitors as in vitro models of 3-dimensional heterotypic segregation and developed a quantitative analysis of their dynamics based on 3D time-lapse microscopy. We show that general inhibition of actomyosin contractility by the Rho kinase inhibitor Y27632 delays segregation. Cell type-specific inhibition of non-muscle myosin2 activity by overexpression of myosin assembly inhibitor S100A4 reduces tissue surface tension, manifested in decreased compaction during aggregation and inverted geometry observed during segregation. The same is observed when we express a constitutively active Rho kinase isoform to ubiquitously keep actomyosin contractility high at cell-cell and cell-medium interfaces and thus overriding the interface-specific regulation of cortical tensions. Tissue surface tension regulation can become an effective tool in tissue engineering."}]},{"ddc":["570"],"date_updated":"2023-12-13T12:09:20Z","department":[{"_id":"MaLo"}],"file_date_updated":"2023-08-14T07:57:55Z","_id":"14039","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"creator":"dernst","date_updated":"2023-08-14T07:57:55Z","file_size":3184217,"date_created":"2023-08-14T07:57:55Z","file_name":"2023_DevelopmentalCell_Leonard.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d8c5dc97cd40c26da2ec98ae723ab368","file_id":"14049","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"publication_status":"published","volume":58,"issue":"15","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Membranes are essential for life. They act as semi-permeable boundaries that define cells and organelles. In addition, their surfaces actively participate in biochemical reaction networks, where they confine proteins, align reaction partners, and directly control enzymatic activities. Membrane-localized reactions shape cellular membranes, define the identity of organelles, compartmentalize biochemical processes, and can even be the source of signaling gradients that originate at the plasma membrane and reach into the cytoplasm and nucleus. The membrane surface is, therefore, an essential platform upon which myriad cellular processes are scaffolded. In this review, we summarize our current understanding of the biophysics and biochemistry of membrane-localized reactions with particular focus on insights derived from reconstituted and cellular systems. We discuss how the interplay of cellular factors results in their self-organization, condensation, assembly, and activity, and the emergent properties derived from them.","lang":"eng"}],"month":"08","intvolume":" 58","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Leonard, Thomas A., et al. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell, vol. 58, no. 15, Elsevier, 2023, pp. 1315–32, doi:10.1016/j.devcel.2023.06.001.","ieee":"T. A. Leonard, M. Loose, and S. Martens, “The membrane surface as a platform that organizes cellular and biochemical processes,” Developmental Cell, vol. 58, no. 15. Elsevier, pp. 1315–1332, 2023.","short":"T.A. Leonard, M. Loose, S. Martens, Developmental Cell 58 (2023) 1315–1332.","ama":"Leonard TA, Loose M, Martens S. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 2023;58(15):1315-1332. doi:10.1016/j.devcel.2023.06.001","apa":"Leonard, T. A., Loose, M., & Martens, S. (2023). The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.001","chicago":"Leonard, Thomas A., Martin Loose, and Sascha Martens. “The Membrane Surface as a Platform That Organizes Cellular and Biochemical Processes.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.001.","ista":"Leonard TA, Loose M, Martens S. 2023. The membrane surface as a platform that organizes cellular and biochemical processes. Developmental Cell. 58(15), 1315–1332."},"title":"The membrane surface as a platform that organizes cellular and biochemical processes","author":[{"first_name":"Thomas A.","last_name":"Leonard","full_name":"Leonard, Thomas A."},{"last_name":"Loose","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Martens, Sascha","last_name":"Martens","first_name":"Sascha"}],"external_id":{"isi":["001059110400001"],"pmid":["37419118"]},"article_processing_charge":"Yes (via OA deal)","project":[{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","grant_number":"P34607","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d"},{"_id":"bd6ae2ca-d553-11ed-ba76-a4aa239da5ee","grant_number":"101045340","name":"Synthetic and structural biology of Rab GTPase networks"}],"day":"07","publication":"Developmental Cell","has_accepted_license":"1","isi":1,"year":"2023","date_published":"2023-08-07T00:00:00Z","doi":"10.1016/j.devcel.2023.06.001","date_created":"2023-08-13T22:01:12Z","page":"1315-1332","acknowledgement":"We acknowledge funding from the Austrian Science Fund (FWF F79, P32814-B, and P35061-B to S.M.; P34607-B to M.L.; and P30584-B and P33066-B to T.A.L.) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 101045340 to M.L.). We are grateful for comments on the manuscript by Justyna Sawa-Makarska, Verena Baumann, Marko Kojic, Philipp Radler, Ronja Reinhardt, and Sumire Antonioli.","quality_controlled":"1","publisher":"Elsevier","oa":1},{"date_created":"2023-08-13T22:01:13Z","doi":"10.1038/s41467-023-40388-6","date_published":"2023-08-04T00:00:00Z","publication":"Nature Communications","day":"04","year":"2023","has_accepted_license":"1","isi":1,"oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"P.J.N. and J.W.M. are grateful for the support of the Biotechnology & Biological Sciences Research Council (awards BB/L003260/1 and BB/P00931X/1). J. Knoppová, R.S. and J. Komenda were supported by the Czech Science Foundation (project 19-29225X) and by ERC project Photoredesign (no. 854126) and L.A.S. was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron Microscopy Facility (EMF), the Life Science Facility (LSF) and the IST high-performance computing cluster.","title":"The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis","article_processing_charge":"Yes","external_id":{"isi":["001042606700004"]},"author":[{"first_name":"Ziyu","full_name":"Zhao, Ziyu","last_name":"Zhao"},{"orcid":"0000-0001-5618-3449","full_name":"Vercellino, Irene","last_name":"Vercellino","id":"3ED6AF16-F248-11E8-B48F-1D18A9856A87","first_name":"Irene"},{"full_name":"Knoppová, Jana","last_name":"Knoppová","first_name":"Jana"},{"full_name":"Sobotka, Roman","last_name":"Sobotka","first_name":"Roman"},{"first_name":"James W.","last_name":"Murray","full_name":"Murray, James W."},{"first_name":"Peter J.","last_name":"Nixon","full_name":"Nixon, Peter J."},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"},{"full_name":"Komenda, Josef","last_name":"Komenda","first_name":"Josef"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Zhao, Ziyu, et al. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications, vol. 14, 4681, Springer Nature, 2023, doi:10.1038/s41467-023-40388-6.","short":"Z. Zhao, I. Vercellino, J. Knoppová, R. Sobotka, J.W. Murray, P.J. Nixon, L.A. Sazanov, J. Komenda, Nature Communications 14 (2023).","ieee":"Z. Zhao et al., “The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis,” Nature Communications, vol. 14. Springer Nature, 2023.","ama":"Zhao Z, Vercellino I, Knoppová J, et al. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 2023;14. doi:10.1038/s41467-023-40388-6","apa":"Zhao, Z., Vercellino, I., Knoppová, J., Sobotka, R., Murray, J. W., Nixon, P. J., … Komenda, J. (2023). The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-40388-6","chicago":"Zhao, Ziyu, Irene Vercellino, Jana Knoppová, Roman Sobotka, James W. Murray, Peter J. Nixon, Leonid A Sazanov, and Josef Komenda. “The Ycf48 Accessory Factor Occupies the Site of the Oxygen-Evolving Manganese Cluster during Photosystem II Biogenesis.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-40388-6.","ista":"Zhao Z, Vercellino I, Knoppová J, Sobotka R, Murray JW, Nixon PJ, Sazanov LA, Komenda J. 2023. The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis. Nature Communications. 14, 4681."},"article_number":"4681","volume":14,"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14044","checksum":"3b9043df3d51c300f9be95eac3ff9d0b","file_size":2315325,"date_updated":"2023-08-14T07:01:12Z","creator":"dernst","file_name":"2023_NatureComm_Zhao.pdf","date_created":"2023-08-14T07:01:12Z"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"intvolume":" 14","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we use cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the water-oxidising Mn4CaO5 cluster, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides valuable insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"department":[{"_id":"LeSa"}],"file_date_updated":"2023-08-14T07:01:12Z","ddc":["570"],"date_updated":"2023-12-13T12:06:56Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14040"},{"volume":2023,"publication_status":"published","publication_identifier":{"issn":["1043-6871"],"isbn":["9798350335873"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.09930"}],"scopus_import":"1","intvolume":" 2023","month":"07","abstract":[{"text":"A classic solution technique for Markov decision processes (MDP) and stochastic games (SG) is value iteration (VI). Due to its good practical performance, this approximative approach is typically preferred over exact techniques, even though no practical bounds on the imprecision of the result could be given until recently. As a consequence, even the most used model checkers could return arbitrarily wrong results. Over the past decade, different works derived stopping criteria, indicating when the precision reaches the desired level, for various settings, in particular MDP with reachability, total reward, and mean payoff, and SG with reachability.In this paper, we provide the first stopping criteria for VI on SG with total reward and mean payoff, yielding the first anytime algorithms in these settings. To this end, we provide the solution in two flavours: First through a reduction to the MDP case and second directly on SG. The former is simpler and automatically utilizes any advances on MDP. The latter allows for more local computations, heading towards better practical efficiency.Our solution unifies the previously mentioned approaches for MDP and SG and their underlying ideas. To achieve this, we isolate objective-specific subroutines as well as identify objective-independent concepts. These structural concepts, while surprisingly simple, form the very essence of the unified solution.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_updated":"2023-12-13T12:06:10Z","conference":{"start_date":"2023-06-26","end_date":"2023-06-29","location":"Boston, MA, United States","name":"LICS: Symposium on Logic in Computer Science"},"type":"conference","status":"public","_id":"13967","date_created":"2023-08-06T22:01:10Z","doi":"10.1109/LICS56636.2023.10175771","date_published":"2023-07-01T00:00:00Z","year":"2023","isi":1,"publication":"38th Annual ACM/IEEE Symposium on Logic in Computer Science","day":"01","oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","acknowledgement":"This research was funded in part by DFG projects 383882557 “SUV” and 427755713 “GOPro”.","external_id":{"isi":["001036707700042"],"arxiv":["2304.09930"]},"article_processing_charge":"No","author":[{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165"},{"full_name":"Weininger, Maximilian","last_name":"Weininger","id":"02ab0197-cc70-11ed-ab61-918e71f56881","first_name":"Maximilian"}],"title":"Stopping criteria for value iteration on stochastic games with quantitative objectives","citation":{"mla":"Kretinsky, Jan, et al. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” 38th Annual ACM/IEEE Symposium on Logic in Computer Science, vol. 2023, Institute of Electrical and Electronics Engineers, 2023, doi:10.1109/LICS56636.2023.10175771.","ama":"Kretinsky J, Meggendorfer T, Weininger M. Stopping criteria for value iteration on stochastic games with quantitative objectives. In: 38th Annual ACM/IEEE Symposium on Logic in Computer Science. Vol 2023. Institute of Electrical and Electronics Engineers; 2023. doi:10.1109/LICS56636.2023.10175771","apa":"Kretinsky, J., Meggendorfer, T., & Weininger, M. (2023). Stopping criteria for value iteration on stochastic games with quantitative objectives. In 38th Annual ACM/IEEE Symposium on Logic in Computer Science (Vol. 2023). Boston, MA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/LICS56636.2023.10175771","short":"J. Kretinsky, T. Meggendorfer, M. Weininger, in:, 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Institute of Electrical and Electronics Engineers, 2023.","ieee":"J. Kretinsky, T. Meggendorfer, and M. Weininger, “Stopping criteria for value iteration on stochastic games with quantitative objectives,” in 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Boston, MA, United States, 2023, vol. 2023.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, and Maximilian Weininger. “Stopping Criteria for Value Iteration on Stochastic Games with Quantitative Objectives.” In 38th Annual ACM/IEEE Symposium on Logic in Computer Science, Vol. 2023. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/LICS56636.2023.10175771.","ista":"Kretinsky J, Meggendorfer T, Weininger M. 2023. Stopping criteria for value iteration on stochastic games with quantitative objectives. 38th Annual ACM/IEEE Symposium on Logic in Computer Science. LICS: Symposium on Logic in Computer Science vol. 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_created":"2023-08-06T22:01:10Z","doi":"10.1016/j.gde.2023.102087","date_published":"2023-08-01T00:00:00Z","year":"2023","isi":1,"has_accepted_license":"1","publication":"Current Opinion in Genetics and Development","day":"01","oa":1,"quality_controlled":"1","publisher":"Elsevier","external_id":{"isi":["001047020200001"],"pmid":["37441873"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Hollwey","full_name":"Hollwey, Elizabeth","first_name":"Elizabeth","id":"b8c4f54b-e484-11eb-8fdc-a54df64ef6dd"},{"first_name":"Amy","last_name":"Briffa","full_name":"Briffa, Amy"},{"first_name":"Martin","full_name":"Howard, Martin","last_name":"Howard"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"title":"Concepts, mechanisms and implications of long-term epigenetic inheritance","citation":{"mla":"Hollwey, Elizabeth, et al. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development, vol. 81, no. 8, 102087, Elsevier, 2023, doi:10.1016/j.gde.2023.102087.","ama":"Hollwey E, Briffa A, Howard M, Zilberman D. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 2023;81(8). doi:10.1016/j.gde.2023.102087","apa":"Hollwey, E., Briffa, A., Howard, M., & Zilberman, D. (2023). Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. Elsevier. https://doi.org/10.1016/j.gde.2023.102087","short":"E. Hollwey, A. Briffa, M. Howard, D. Zilberman, Current Opinion in Genetics and Development 81 (2023).","ieee":"E. Hollwey, A. Briffa, M. Howard, and D. Zilberman, “Concepts, mechanisms and implications of long-term epigenetic inheritance,” Current Opinion in Genetics and Development, vol. 81, no. 8. Elsevier, 2023.","chicago":"Hollwey, Elizabeth, Amy Briffa, Martin Howard, and Daniel Zilberman. “Concepts, Mechanisms and Implications of Long-Term Epigenetic Inheritance.” Current Opinion in Genetics and Development. Elsevier, 2023. https://doi.org/10.1016/j.gde.2023.102087.","ista":"Hollwey E, Briffa A, Howard M, Zilberman D. 2023. Concepts, mechanisms and implications of long-term epigenetic inheritance. Current Opinion in Genetics and Development. 81(8), 102087."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"102087","issue":"8","volume":81,"publication_identifier":{"eissn":["1879-0380"],"issn":["0959-437X"]},"language":[{"iso":"eng"}],"file":[{"success":1,"checksum":"a294cd9506b80ed6ef218ef44ed32765","file_id":"13980","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_CurrentOpinionGenetics_Hollwey.pdf","date_created":"2023-08-07T08:32:26Z","creator":"dernst","file_size":2568632,"date_updated":"2023-08-07T08:32:26Z"}],"scopus_import":"1","intvolume":" 81","month":"08","abstract":[{"lang":"eng","text":"Many modes and mechanisms of epigenetic inheritance have been elucidated in eukaryotes. Most of them are relatively short-term, generally not exceeding one or a few organismal generations. However, emerging evidence indicates that one mechanism, cytosine DNA methylation, can mediate epigenetic inheritance over much longer timescales, which are mostly or completely inaccessible in the laboratory. Here we discuss the evidence for, and mechanisms and implications of, such long-term epigenetic inheritance. We argue that compelling evidence supports the long-term epigenetic inheritance of gene body methylation, at least in the model angiosperm Arabidopsis thaliana, and that variation in such methylation can therefore serve as an epigenetic basis for phenotypic variation in natural populations."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"DaZi"}],"file_date_updated":"2023-08-07T08:32:26Z","date_updated":"2023-12-13T12:05:31Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"13965"},{"language":[{"iso":"eng"}],"file":[{"relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"14075","checksum":"4e44e169f2724ee8c9324cd60bcc2b71","creator":"gpuixeus","file_size":10891454,"date_updated":"2023-08-17T06:55:24Z","file_name":"Thesis_latex_forpdfa.zip","date_created":"2023-08-16T18:15:17Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"e10b04cd8f3fecc0d9ef6e6868b6e1e8","file_id":"14079","success":1,"date_updated":"2023-08-18T10:47:55Z","file_size":19856686,"creator":"gpuixeus","date_created":"2023-08-18T10:47:55Z","file_name":"PhDThesis_PuixeuG.pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-035-0"],"issn":["2663-337X"]},"ec_funded":1,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9803"},{"relation":"research_data","status":"public","id":"12933"},{"relation":"part_of_dissertation","status":"public","id":"6831"},{"relation":"part_of_dissertation","status":"public","id":"14077"}]},"oa_version":"Published Version","abstract":[{"text":"Females and males across species are subject to divergent selective pressures arising\r\nfrom di↵erent reproductive interests and ecological niches. This often translates into a\r\nintricate array of sex-specific natural and sexual selection on traits that have a shared\r\ngenetic basis between both sexes, causing a genetic sexual conflict. The resolution of\r\nthis conflict mostly relies on the evolution of sex-specific expression of the shared genes,\r\nleading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought\r\nto evolve via modifications of the genetic networks ultimately linked to sex-determining\r\ntranscription factors. Although much empirical and theoretical evidence supports this\r\nstandard picture of the molecular basis of sexual conflict resolution, there still are a\r\nfew open questions regarding the complex array of selective forces driving phenotypic\r\ndi↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis.\r\nFirst, how do patterns of phenotypic sexual dimorphism vary within populations,\r\nas a response to the temporal and spatial changes in sex-specific selective forces? To\r\ntackle this question, I analyze the patterns of sex-specific phenotypic variation along\r\nthree life stages and across populations spanning the whole geographical range of Rumex\r\nhastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis.\r\nSecond, how do gene expression patterns lead to phenotypic dimorphism, and what\r\nare the molecular mechanisms underlying the observed transcriptomic variation? I\r\naddress this question by examining the sex- and tissue-specific expression variation in\r\nnewly-generated datasets of sex-specific expression in heads and gonads of Drosophila\r\nmelanogaster. I additionally used two complementary approaches for the study of the\r\ngenetic basis of sex di↵erences in gene expression in the second and third Chapters of\r\nthe thesis.\r\nThird, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual\r\ndimorphism? I develop models of sex-specific stabilizing selection, mutation and drift\r\nto formalize common intuition regarding the patterns of covariation between intersex\r\ncorrelation and sexual dimorphism in the fourth Chapter of the thesis.\r\nAlltogether, the work described in this PhD thesis provides useful insights into the\r\nlinks between genetic, transcriptomic and phenotypic layers of sex-specific variation,\r\nand contributes to our general understanding of the dynamics of sexual dimorphism\r\nevolution.","lang":"eng"}],"month":"08","alternative_title":["ISTA Thesis"],"ddc":["576"],"date_updated":"2023-12-13T12:15:36Z","supervisor":[{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","full_name":"Vicoso, Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2023-08-18T10:47:55Z","_id":"14058","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"dissertation","day":"15","year":"2023","has_accepted_license":"1","date_created":"2023-08-15T10:20:40Z","date_published":"2023-08-15T00:00:00Z","doi":"10.15479/at:ista:14058","page":"230","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Puixeu Sala G. 2023. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria.","chicago":"Puixeu Sala, Gemma. “The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14058.","ieee":"G. Puixeu Sala, “The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation,” Institute of Science and Technology Austria, 2023.","short":"G. Puixeu Sala, The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation, Institute of Science and Technology Austria, 2023.","apa":"Puixeu Sala, G. (2023). The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14058","ama":"Puixeu Sala G. The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation. 2023. doi:10.15479/at:ista:14058","mla":"Puixeu Sala, Gemma. The Molecular Basis of Sexual Dimorphism: Experimental and Theoretical Characterization of Phenotypic, Transcriptomic and Genetic Patterns of Sex-Specific Adaptation. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14058."},"title":"The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation","article_processing_charge":"No","author":[{"orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma","last_name":"Puixeu Sala","first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}]},{"_id":"14077","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Genetics (clinical)","Genetics","Molecular Biology"],"date_updated":"2023-12-13T12:15:37Z","ddc":["570"],"file_date_updated":"2023-11-07T09:00:19Z","department":[{"_id":"BeVi"},{"_id":"NiBa"},{"_id":"GradSch"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"text":"The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed\r\nso far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues\r\nand biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila\r\nmelanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate\r\ncrosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand,\r\ntestes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that\r\nhave been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation\r\nof genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression\r\nand can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis\r\nvariation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary\r\nexpression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance\r\nas well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled\r\nexperimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 13","publication_identifier":{"issn":["2160-1836"]},"publication_status":"published","file":[{"success":1,"file_id":"14498","checksum":"c62e29fc7c5efbf8356f4c60cab4a2d1","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_G3_Puixeu.pdf","date_created":"2023-11-07T09:00:19Z","creator":"dernst","file_size":845642,"date_updated":"2023-11-07T09:00:19Z"}],"language":[{"iso":"eng"}],"volume":13,"issue":"8","related_material":{"record":[{"relation":"research_data","id":"12933","status":"public"},{"relation":"dissertation_contains","id":"14058","status":"public"}]},"ec_funded":1,"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"_id":"9B9DFC9E-BA93-11EA-9121-9846C619BF3A","name":"Sexual conflict: resolution, constraints and biomedical implications","grant_number":"25817"}],"citation":{"ista":"Puixeu Sala G, Macon A, Vicoso B. 2023. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 13(8).","chicago":"Puixeu Sala, Gemma, Ariana Macon, and Beatriz Vicoso. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics. Oxford University Press, 2023. https://doi.org/10.1093/g3journal/jkad121.","apa":"Puixeu Sala, G., Macon, A., & Vicoso, B. (2023). Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. Oxford University Press. https://doi.org/10.1093/g3journal/jkad121","ama":"Puixeu Sala G, Macon A, Vicoso B. Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. G3: Genes, Genomes, Genetics. 2023;13(8). doi:10.1093/g3journal/jkad121","short":"G. Puixeu Sala, A. Macon, B. Vicoso, G3: Genes, Genomes, Genetics 13 (2023).","ieee":"G. Puixeu Sala, A. Macon, and B. Vicoso, “Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster,” G3: Genes, Genomes, Genetics, vol. 13, no. 8. Oxford University Press, 2023.","mla":"Puixeu Sala, Gemma, et al. “Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” G3: Genes, Genomes, Genetics, vol. 13, no. 8, Oxford University Press, 2023, doi:10.1093/g3journal/jkad121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"},{"last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz"}],"article_processing_charge":"Yes","external_id":{"isi":["001002997200001"]},"title":"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","acknowledgement":"We thank members of the Vicoso Group for comments on the manuscript, the Scientific Computing Unit at ISTA for technical support, and 2 anonymous reviewers for useful feedback. GP is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology Austria (DOC 25817) and received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant (agreement no. 665385).","publisher":"Oxford University Press","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"G3: Genes, Genomes, Genetics","date_published":"2023-08-01T00:00:00Z","doi":"10.1093/g3journal/jkad121","date_created":"2023-08-18T06:52:14Z"},{"date_created":"2023-08-20T22:01:13Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1242/jcs.260668","year":"2023","has_accepted_license":"1","isi":1,"publication":"Journal of Cell Science","day":"01","publisher":"The Company of Biologists","quality_controlled":"1","acknowledgement":"The authors thank their respective lab members for feedback and helpful discussions. We thank the bioimaging and zebrafish facilities of IST Austria for their support.\r\nThis work was supported by the National Institutes of Health [R01GM112794 to A.L.M.], by Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science [21K06156 to T.H.], by the Grant Program for Biomedical Engineering Research from the Nakatani Foundation for Advancement of Measuring Technologies in Biomedical Engineering [to T.H.] and by funding from the European Research Council [advanced grant 742573 to C.-P.H.]. ","article_processing_charge":"No","external_id":{"isi":["001070149000001"]},"author":[{"full_name":"Higashi, Tomohito","last_name":"Higashi","first_name":"Tomohito"},{"full_name":"Stephenson, Rachel E.","last_name":"Stephenson","first_name":"Rachel E."},{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","last_name":"Schwayer"},{"full_name":"Huljev, Karla","last_name":"Huljev","id":"44C6F6A6-F248-11E8-B48F-1D18A9856A87","first_name":"Karla"},{"first_name":"Atsuko Y.","last_name":"Higashi","full_name":"Higashi, Atsuko Y."},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chiba","full_name":"Chiba, Hideki","first_name":"Hideki"},{"first_name":"Ann L.","last_name":"Miller","full_name":"Miller, Ann L."}],"title":"ZnUMBA - a live imaging method to detect local barrier breaches","citation":{"mla":"Higashi, Tomohito, et al. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science, vol. 136, no. 15, jcs260668, The Company of Biologists, 2023, doi:10.1242/jcs.260668.","apa":"Higashi, T., Stephenson, R. E., Schwayer, C., Huljev, K., Higashi, A. Y., Heisenberg, C.-P. J., … Miller, A. L. (2023). ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. The Company of Biologists. https://doi.org/10.1242/jcs.260668","ama":"Higashi T, Stephenson RE, Schwayer C, et al. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 2023;136(15). doi:10.1242/jcs.260668","short":"T. Higashi, R.E. Stephenson, C. Schwayer, K. Huljev, A.Y. Higashi, C.-P.J. Heisenberg, H. Chiba, A.L. Miller, Journal of Cell Science 136 (2023).","ieee":"T. Higashi et al., “ZnUMBA - a live imaging method to detect local barrier breaches,” Journal of Cell Science, vol. 136, no. 15. The Company of Biologists, 2023.","chicago":"Higashi, Tomohito, Rachel E. Stephenson, Cornelia Schwayer, Karla Huljev, Atsuko Y. Higashi, Carl-Philipp J Heisenberg, Hideki Chiba, and Ann L. Miller. “ZnUMBA - a Live Imaging Method to Detect Local Barrier Breaches.” Journal of Cell Science. The Company of Biologists, 2023. https://doi.org/10.1242/jcs.260668.","ista":"Higashi T, Stephenson RE, Schwayer C, Huljev K, Higashi AY, Heisenberg C-PJ, Chiba H, Miller AL. 2023. ZnUMBA - a live imaging method to detect local barrier breaches. Journal of Cell Science. 136(15), jcs260668."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","call_identifier":"H2020","_id":"260F1432-B435-11E9-9278-68D0E5697425"}],"article_number":"jcs260668","ec_funded":1,"volume":136,"issue":"15","publication_status":"published","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_JourCellScience_Higashi.pdf","date_created":"2023-08-21T07:37:54Z","creator":"dernst","file_size":18665315,"date_updated":"2023-08-21T07:37:54Z","embargo":"2024-08-10","file_id":"14092","checksum":"a399389b7e3d072f1788b63e612a10b3","relation":"main_file","access_level":"closed","embargo_to":"open_access","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 136","month":"08","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Epithelial barrier function is commonly analyzed using transepithelial electrical resistance, which measures ion flux across a monolayer, or by adding traceable macromolecules and monitoring their passage across the monolayer. Although these methods measure changes in global barrier function, they lack the sensitivity needed to detect local or transient barrier breaches, and they do not reveal the location of barrier leaks. Therefore, we previously developed a method that we named the zinc-based ultrasensitive microscopic barrier assay (ZnUMBA), which overcomes these limitations, allowing for detection of local tight junction leaks with high spatiotemporal resolution. Here, we present expanded applications for ZnUMBA. ZnUMBA can be used in Xenopus embryos to measure the dynamics of barrier restoration and actin accumulation following laser injury. ZnUMBA can also be effectively utilized in developing zebrafish embryos as well as cultured monolayers of Madin–Darby canine kidney (MDCK) II epithelial cells. ZnUMBA is a powerful and flexible method that, with minimal optimization, can be applied to multiple systems to measure dynamic changes in barrier function with spatiotemporal precision."}],"oa_version":"None","file_date_updated":"2023-08-21T07:37:54Z","department":[{"_id":"CaHe"},{"_id":"EvBe"}],"date_updated":"2023-12-13T12:11:18Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"14082"},{"title":"Practical limitations of Ethereum’s layer-2","article_processing_charge":"Yes","external_id":{"isi":["000927831000001"]},"author":[{"first_name":"Ray","id":"f09651b9-fec0-11ec-b5d8-934aff0e52a4","orcid":"0000-0001-7227-8309","full_name":"Neiheiser, Ray","last_name":"Neiheiser"},{"first_name":"Gustavo","full_name":"Inacio, Gustavo","last_name":"Inacio"},{"last_name":"Rech","full_name":"Rech, Luciana","first_name":"Luciana"},{"first_name":"Carlos","full_name":"Montez, Carlos","last_name":"Montez"},{"first_name":"Miguel","full_name":"Matos, Miguel","last_name":"Matos"},{"last_name":"Rodrigues","full_name":"Rodrigues, Luis","first_name":"Luis"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Neiheiser, Ray, Gustavo Inacio, Luciana Rech, Carlos Montez, Miguel Matos, and Luis Rodrigues. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/access.2023.3237897.","ista":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. 2023. Practical limitations of Ethereum’s layer-2. IEEE Access. 11, 8651–8662.","mla":"Neiheiser, Ray, et al. “Practical Limitations of Ethereum’s Layer-2.” IEEE Access, vol. 11, Institute of Electrical and Electronics Engineers, 2023, pp. 8651–62, doi:10.1109/access.2023.3237897.","apa":"Neiheiser, R., Inacio, G., Rech, L., Montez, C., Matos, M., & Rodrigues, L. (2023). Practical limitations of Ethereum’s layer-2. IEEE Access. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/access.2023.3237897","ama":"Neiheiser R, Inacio G, Rech L, Montez C, Matos M, Rodrigues L. Practical limitations of Ethereum’s layer-2. IEEE Access. 2023;11:8651-8662. doi:10.1109/access.2023.3237897","short":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, L. Rodrigues, IEEE Access 11 (2023) 8651–8662.","ieee":"R. Neiheiser, G. Inacio, L. Rech, C. Montez, M. Matos, and L. Rodrigues, “Practical limitations of Ethereum’s layer-2,” IEEE Access, vol. 11. Institute of Electrical and Electronics Engineers, pp. 8651–8662, 2023."},"oa":1,"quality_controlled":"1","publisher":"Institute of Electrical and Electronics Engineers","acknowledgement":"This work was supported in part by the Coordenação de Aperfeiçoamento de Pessoal de Nivel Superior (CAPES)—Brazil (CAPES), in part by the Fundação para a Ciência e Tecnologia (FCT) under Project UIDB/50021/2020 and Grant 2020.05270.BD, in part by the Project COSMOS (via the Orçamento de Estado (OE) with ref. PTDC/EEI-COM/29271/2017 and via the ‘‘Programa Operacional Regional de Lisboa na sua componente Fundo Europeu de Desenvolvimento Regional (FEDER)’’ with ref. Lisboa-01-0145-FEDER-029271), and in part by the project Angainor with reference LISBOA-01-0145-FEDER-031456 as well as supported by Meta Platforms for the project key Transparency at Scale.","date_created":"2023-08-09T12:09:57Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1109/access.2023.3237897","page":"8651-8662","publication":"IEEE Access","day":"01","year":"2023","isi":1,"has_accepted_license":"1","keyword":["General Engineering","General Materials Science","General Computer Science","Electrical and Electronic Engineering"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13988","file_date_updated":"2023-08-22T06:37:48Z","department":[{"_id":"ElKo"}],"ddc":["000"],"date_updated":"2023-12-13T12:14:52Z","intvolume":" 11","month":"08","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Most permissionless blockchains inherently suffer from throughput limitations. Layer-2 systems, such as side-chains or Rollups, have been proposed as a possible strategy to overcome this limitation. Layer-2 systems interact with the main-chain in two ways. First, users can move funds from/to the main-chain to/from the layer-2. Second, layer-2 systems periodically synchronize with the main-chain to keep some form of log of their activity on the main-chain - this log is key for security. Due to this interaction with the main-chain, which is necessary and recurrent, layer-2 systems impose some load on the main-chain. The impact of such load on the main-chain has been, so far, poorly understood. In addition to that, layer-2 approaches typically sacrifice decentralization and security in favor of higher throughput. This paper presents an experimental study that analyzes the current state of Ethereum layer-2 projects. Our goal is to assess the load they impose on Ethereum and to understand their scalability potential in the long-run. Our analysis shows that the impact of any given layer-2 on the main-chain is the result of both technical aspects (how state is logged on the main-chain) and user behavior (how often users decide to transfer funds between the layer-2 and the main-chain). Based on our observations, we infer that without efficient mechanisms that allow users to transfer funds in a secure and fast manner directly from one layer-2 project to another, current layer-2 systems will not be able to scale Ethereum effectively, regardless of their technical solutions. Furthermore, from our results, we conclude that the layer-2 systems that offer similar security guarantees as Ethereum have limited scalability potential, while approaches that offer better performance, sacrifice security and lead to an increase in centralization which runs against the end-goals of permissionless blockchains.","lang":"eng"}],"volume":11,"language":[{"iso":"eng"}],"file":[{"file_id":"14166","checksum":"4b80b0ff212edf7e5842fbdd53784432","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-08-22T06:37:48Z","file_name":"2023_IEEEAccess_Neiheiser.pdf","creator":"dernst","date_updated":"2023-08-22T06:37:48Z","file_size":1289285}],"publication_status":"published","publication_identifier":{"issn":["2169-3536"]}},{"date_updated":"2023-12-13T12:15:36Z","citation":{"mla":"Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.","apa":"Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933","ama":"Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933","ieee":"G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.","short":"G. Puixeu Sala, (2023).","chicago":"Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.","ista":"Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"author":[{"first_name":"Gemma","id":"33AB266C-F248-11E8-B48F-1D18A9856A87","last_name":"Puixeu Sala","orcid":"0000-0001-8330-1754","full_name":"Puixeu Sala, Gemma"}],"article_processing_charge":"No","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"BeVi"}],"file_date_updated":"2023-05-11T12:50:18Z","title":"Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster","_id":"12933","type":"research_data","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","has_accepted_license":"1","year":"2023","file":[{"file_id":"12934","checksum":"0ba0bcd0bb8b18d84792136a4370df90","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/csv","date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S1.csv","creator":"gpuixeus","date_updated":"2023-05-10T09:41:43Z","file_size":8029982},{"date_created":"2023-05-10T09:41:43Z","file_name":"Dataset_S2.csv","creator":"gpuixeus","date_updated":"2023-05-10T09:41:43Z","file_size":13667640,"file_id":"12935","checksum":"a62aa9a6d4904e0fdb699cf752640863","success":1,"access_level":"open_access","relation":"main_file","content_type":"text/csv"},{"creator":"gpuixeus","file_size":8369141,"date_updated":"2023-05-10T09:41:48Z","file_name":"Dataset_S3.csv","date_created":"2023-05-10T09:41:48Z","relation":"main_file","access_level":"open_access","content_type":"text/csv","success":1,"checksum":"e20ea7f4f8a9bdf1b3849a44664ae58b","file_id":"12936"},{"access_level":"open_access","relation":"main_file","content_type":"text/csv","file_id":"12937","checksum":"f6156e5fc44446c907ddd0d7289d4cf8","success":1,"creator":"gpuixeus","date_updated":"2023-05-10T09:41:50Z","file_size":19543247,"date_created":"2023-05-10T09:41:50Z","file_name":"Dataset_S4.csv"},{"file_size":4566,"date_updated":"2023-05-11T12:50:18Z","creator":"gpuixeus","file_name":"readme.txt","date_created":"2023-05-11T12:50:18Z","content_type":"text/plain","relation":"main_file","access_level":"open_access","success":1,"checksum":"ae9f54c77a1c42b666ae6c1dfd33ac86","file_id":"12944"}],"day":"15","doi":"10.15479/AT:ISTA:12933","related_material":{"record":[{"id":"14058","status":"public","relation":"used_in_publication"},{"relation":"used_in_publication","id":"14077","status":"public"}]},"date_published":"2023-05-15T00:00:00Z","date_created":"2023-05-10T10:00:49Z","contributor":[{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"abstract":[{"text":"Datasets of the publication \"Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster\".","lang":"eng"}],"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","oa":1,"month":"05"},{"_id":"14245","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-12-13T12:19:42Z","ddc":["510"],"department":[{"_id":"TiBr"}],"file_date_updated":"2023-09-05T07:26:17Z","abstract":[{"lang":"eng","text":"We establish effective counting results for lattice points in families of domains in real, complex and quaternionic hyperbolic spaces of any dimension. The domains we focus on are defined as product sets with respect to an Iwasawa decomposition. Several natural diophantine problems can be reduced to counting lattice points in such domains. These include equidistribution of the ratio of the length of the shortest solution (x,y) to the gcd equation bx−ay=1 relative to the length of (a,b), where (a,b) ranges over primitive vectors in a disc whose radius increases, the natural analog of this problem in imaginary quadratic number fields, as well as equidistribution of integral solutions to the diophantine equation defined by an integral Lorentz form in three or more variables. We establish an effective rate of convergence for these equidistribution problems, depending on the size of the spectral gap associated with a suitable lattice subgroup in the isometry group of the relevant hyperbolic space. The main result underlying our discussion amounts to establishing effective joint equidistribution for the horospherical component and the radial component in the Iwasawa decomposition of lattice elements."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 324","month":"07","publication_status":"published","publication_identifier":{"eissn":["1945-5844"],"issn":["0030-8730"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"a675b53cfb31fa46be1e879b7e77fe8c","file_id":"14267","creator":"dernst","file_size":654895,"date_updated":"2023-09-05T07:26:17Z","file_name":"2023_PacificJourMaths_Horesh.pdf","date_created":"2023-09-05T07:26:17Z"}],"volume":324,"issue":"2","citation":{"chicago":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics. Mathematical Sciences Publishers, 2023. https://doi.org/10.2140/pjm.2023.324.265.","ista":"Horesh T, Nevo A. 2023. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 324(2), 265–294.","mla":"Horesh, Tal, and Amos Nevo. “Horospherical Coordinates of Lattice Points in Hyperbolic Spaces: Effective Counting and Equidistribution.” Pacific Journal of Mathematics, vol. 324, no. 2, Mathematical Sciences Publishers, 2023, pp. 265–94, doi:10.2140/pjm.2023.324.265.","ieee":"T. Horesh and A. Nevo, “Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution,” Pacific Journal of Mathematics, vol. 324, no. 2. Mathematical Sciences Publishers, pp. 265–294, 2023.","short":"T. Horesh, A. Nevo, Pacific Journal of Mathematics 324 (2023) 265–294.","apa":"Horesh, T., & Nevo, A. (2023). Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. Mathematical Sciences Publishers. https://doi.org/10.2140/pjm.2023.324.265","ama":"Horesh T, Nevo A. Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution. Pacific Journal of Mathematics. 2023;324(2):265-294. doi:10.2140/pjm.2023.324.265"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"arxiv":["1612.08215"],"isi":["001047690500001"]},"author":[{"full_name":"Horesh, Tal","last_name":"Horesh","id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425","first_name":"Tal"},{"full_name":"Nevo, Amos","last_name":"Nevo","first_name":"Amos"}],"title":"Horospherical coordinates of lattice points in hyperbolic spaces: Effective counting and equidistribution","acknowledgement":"The authors thank the referee for important comments which led to significant improvements is the presentation of several results in the paper. They also thank Ami Paz for preparing the figures for this paper. Horesh thanks Ami Paz and Yakov Karasik for helpful discussions. Nevo thanks John Parker and Rene Rühr for providing some very useful references. Nevo is supported by ISF Grant No. 2095/15.","oa":1,"quality_controlled":"1","publisher":"Mathematical Sciences Publishers","year":"2023","isi":1,"has_accepted_license":"1","publication":"Pacific Journal of Mathematics","day":"26","page":"265-294","date_created":"2023-08-27T22:01:18Z","doi":"10.2140/pjm.2023.324.265","date_published":"2023-07-26T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Brauneis, Fabian, Areg Ghazaryan, Hans-Werner Hammer, and Artem Volosniev. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics. Springer Nature, 2023. https://doi.org/10.1038/s42005-023-01281-2.","ista":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. 2023. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 6, 224.","mla":"Brauneis, Fabian, et al. “Emergence of a Bose Polaron in a Small Ring Threaded by the Aharonov-Bohm Flux.” Communications Physics, vol. 6, 224, Springer Nature, 2023, doi:10.1038/s42005-023-01281-2.","apa":"Brauneis, F., Ghazaryan, A., Hammer, H.-W., & Volosniev, A. (2023). Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-023-01281-2","ama":"Brauneis F, Ghazaryan A, Hammer H-W, Volosniev A. Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux. Communications Physics. 2023;6. doi:10.1038/s42005-023-01281-2","short":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, A. Volosniev, Communications Physics 6 (2023).","ieee":"F. Brauneis, A. Ghazaryan, H.-W. Hammer, and A. Volosniev, “Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux,” Communications Physics, vol. 6. Springer Nature, 2023."},"title":"Emergence of a Bose polaron in a small ring threaded by the Aharonov-Bohm flux","author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"first_name":"Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"full_name":"Hammer, Hans-Werner","last_name":"Hammer","first_name":"Hans-Werner"},{"first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2301.10488"],"isi":["001052577500002"]},"article_number":"224","day":"22","publication":"Communications Physics","isi":1,"has_accepted_license":"1","year":"2023","date_published":"2023-08-22T00:00:00Z","doi":"10.1038/s42005-023-01281-2","date_created":"2023-08-28T12:36:49Z","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nWe would like to thank Jonas Jager for sharing his data with us in the early stages of this project. We thank Joachim Brand and Ray Yang for sharing with us data from Yang et al.46. This work has received funding from the DFG Project no. 413495248 [VO 2437/1-1] (F.B., H.-W.H., A.G.V.). We acknowledge support from the Deutsche Forschungsgemeinschaft (DFG - German Research Foundation) and the Open Access Publishing Fund of the Technical University of Darmstadt.","publisher":"Springer Nature","quality_controlled":"1","oa":1,"ddc":["530"],"date_updated":"2023-12-13T12:21:09Z","file_date_updated":"2023-09-05T08:45:49Z","department":[{"_id":"MiLe"}],"_id":"14246","status":"public","keyword":["General Physics and Astronomy"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"6edfc59b0ee7dc406d0968b05236e83d","file_id":"14268","success":1,"date_updated":"2023-09-05T08:45:49Z","file_size":855960,"creator":"dernst","date_created":"2023-09-05T08:45:49Z","file_name":"2023_CommPhysics_Brauneis.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2399-3650"]},"publication_status":"published","volume":6,"oa_version":"Published Version","abstract":[{"text":"The model of a ring threaded by the Aharonov-Bohm flux underlies our understanding of a coupling between gauge potentials and matter. The typical formulation of the model is based upon a single particle picture, and should be extended when interactions with other particles become relevant. Here, we illustrate such an extension for a particle in an Aharonov-Bohm ring subject to interactions with a weakly interacting Bose gas. We show that the ground state of the system can be described using the Bose-polaron concept—a particle dressed by interactions with a bosonic environment. We connect the energy spectrum to the effective mass of the polaron, and demonstrate how to change currents in the system by tuning boson-particle interactions. Our results suggest the Aharonov-Bohm ring as a platform for studying coherence and few- to many-body crossover of quasi-particles that arise from an impurity immersed in a medium.","lang":"eng"}],"month":"08","intvolume":" 6","scopus_import":"1"},{"isi":1,"has_accepted_license":"1","year":"2023","day":"03","publication":"Forum of Mathematics, Sigma","doi":"10.1017/fms.2023.65","date_published":"2023-08-03T00:00:00Z","date_created":"2023-08-27T22:01:16Z","acknowledgement":"We thank Agnieszka Bodzenta-Skibińska, Paolo Cascini, Wahei Hara, Sándor Kovács, Alexander Kuznetsov, Mircea Musta ă, Nebojsa Pavic, Pavel Sechin, and Michael Wemyss for discussions and e-mail correspondence. We also thank the anonymous referee for the helpful comments. M.M. was supported by the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 101034413. E.S. was partially supported by the EPSRC grant EP/T019379/1 “Derived categories and algebraic K-theory of singularities”, and by the ERC Synergy grant “Modern Aspects of Geometry: Categories, Cycles and Cohomology of Hyperkähler Varieties.”\r\n\r\n","quality_controlled":"1","publisher":"Cambridge University Press","oa":1,"citation":{"ista":"Mauri M, Shinder E. 2023. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 11, e66.","chicago":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.65.","short":"M. Mauri, E. Shinder, Forum of Mathematics, Sigma 11 (2023).","ieee":"M. Mauri and E. Shinder, “Homological Bondal-Orlov localization conjecture for rational singularities,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023.","apa":"Mauri, M., & Shinder, E. (2023). Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.65","ama":"Mauri M, Shinder E. Homological Bondal-Orlov localization conjecture for rational singularities. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.65","mla":"Mauri, Mirko, and Evgeny Shinder. “Homological Bondal-Orlov Localization Conjecture for Rational Singularities.” Forum of Mathematics, Sigma, vol. 11, e66, Cambridge University Press, 2023, doi:10.1017/fms.2023.65."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","full_name":"Mauri, Mirko","last_name":"Mauri"},{"first_name":"Evgeny","full_name":"Shinder, Evgeny","last_name":"Shinder"}],"article_processing_charge":"Yes","external_id":{"isi":["001041926700001"],"arxiv":["2212.06786"]},"title":"Homological Bondal-Orlov localization conjecture for rational singularities","article_number":"e66","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"publication_identifier":{"eissn":["2050-5094"]},"publication_status":"published","file":[{"file_name":"2023_ForumMathematics_Mauri.pdf","date_created":"2023-09-05T06:43:11Z","creator":"dernst","file_size":280865,"date_updated":"2023-09-05T06:43:11Z","success":1,"file_id":"14266","checksum":"c36241750cc5cb06890aec0ecdfee626","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"volume":11,"ec_funded":1,"abstract":[{"text":"Given a resolution of rational singularities π:X~→X over a field of characteristic zero, we use a Hodge-theoretic argument to prove that the image of the functor Rπ∗:Db(X~)→Db(X)\r\n between bounded derived categories of coherent sheaves generates Db(X)\r\n as a triangulated category. This gives a weak version of the Bondal–Orlov localization conjecture [BO02], answering a question from [PS21]. The same result is established more generally for proper (not necessarily birational) morphisms π:X~→X , with X~\r\n smooth, satisfying Rπ∗(OX~)=OX .","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 11","date_updated":"2023-12-13T12:18:18Z","ddc":["510"],"file_date_updated":"2023-09-05T06:43:11Z","department":[{"_id":"TaHa"}],"_id":"14239","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"doi":"10.1007/s11040-023-09460-x","date_published":"2023-07-26T00:00:00Z","date_created":"2023-08-22T14:09:47Z","isi":1,"has_accepted_license":"1","year":"2023","day":"26","publication":"Mathematical Physics, Analysis and Geometry","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"D.M. and K.M. thank Robert Seiringer for helpful discussions. Open access funding provided by Institute of Science and Technology (IST Austria). Financial support from the Agence Nationale de la Recherche (ANR) through the projects ANR-17-CE40-0016, ANR-17-CE40-0007-01, ANR-17-EURE-0002 (J.L.) and from the European Union’s Horizon 2020 research and innovation programme under the Maria Skłodowska-Curie grant agreement No. 665386 (K.M.) is gratefully acknowledged.","author":[{"full_name":"Lampart, Jonas","last_name":"Lampart","first_name":"Jonas"},{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d","first_name":"David Johannes"},{"id":"316457FC-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof","full_name":"Mysliwy, Krzysztof","last_name":"Mysliwy"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001032992600001"],"arxiv":["2206.14708"]},"title":"On the global minimum of the energy–momentum relation for the polaron","citation":{"chicago":"Lampart, Jonas, David Johannes Mitrouskas, and Krzysztof Mysliwy. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry. Springer Nature, 2023. https://doi.org/10.1007/s11040-023-09460-x.","ista":"Lampart J, Mitrouskas DJ, Mysliwy K. 2023. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 26(3), 17.","mla":"Lampart, Jonas, et al. “On the Global Minimum of the Energy–Momentum Relation for the Polaron.” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3, 17, Springer Nature, 2023, doi:10.1007/s11040-023-09460-x.","short":"J. Lampart, D.J. Mitrouskas, K. Mysliwy, Mathematical Physics, Analysis and Geometry 26 (2023).","ieee":"J. Lampart, D. J. Mitrouskas, and K. Mysliwy, “On the global minimum of the energy–momentum relation for the polaron,” Mathematical Physics, Analysis and Geometry, vol. 26, no. 3. Springer Nature, 2023.","ama":"Lampart J, Mitrouskas DJ, Mysliwy K. On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. 2023;26(3). doi:10.1007/s11040-023-09460-x","apa":"Lampart, J., Mitrouskas, D. J., & Mysliwy, K. (2023). On the global minimum of the energy–momentum relation for the polaron. Mathematical Physics, Analysis and Geometry. Springer Nature. https://doi.org/10.1007/s11040-023-09460-x"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"17","volume":26,"issue":"3","publication_identifier":{"issn":["1385-0172"],"eissn":["1572-9656"]},"publication_status":"published","file":[{"date_updated":"2023-08-23T10:59:15Z","file_size":317026,"creator":"dernst","date_created":"2023-08-23T10:59:15Z","file_name":"2023_MathPhysics_Lampart.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"f0941cc66cb3ed06a12ca4b7e356cfd6","file_id":"14225","success":1}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"07","intvolume":" 26","abstract":[{"lang":"eng","text":"For the Fröhlich model of the large polaron, we prove that the ground state energy as a function of the total momentum has a unique global minimum at momentum zero. This implies the non-existence of a ground state of the translation invariant Fröhlich Hamiltonian and thus excludes the possibility of a localization transition at finite coupling."}],"oa_version":"Published Version","department":[{"_id":"RoSe"}],"file_date_updated":"2023-08-23T10:59:15Z","date_updated":"2023-12-13T12:16:19Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Geometry and Topology","Mathematical Physics"],"_id":"14192"},{"month":"08","intvolume":" 131","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2308.15247"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We demonstrate that a sodium dimer, Na2(13Σ+u), residing on the surface of a helium nanodroplet, can be set into rotation by a nonresonant 1.0 ps infrared laser pulse. The time-dependent degree of alignment measured, exhibits a periodic, gradually decreasing structure that deviates qualitatively from that expected for gas-phase dimers. Comparison to alignment dynamics calculated from the time-dependent rotational Schrödinger equation shows that the deviation is due to the alignment dependent interaction between the dimer and the droplet surface. This interaction confines the dimer to the tangential plane of the droplet surface at the point where it resides and is the reason that the observed alignment dynamics is also well described by a 2D quantum rotor model."}],"issue":"5","volume":131,"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"publication_status":"published","status":"public","type":"journal_article","article_type":"original","_id":"14238","department":[{"_id":"MiLe"}],"date_updated":"2023-12-13T12:18:54Z","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"H. S. acknowledges support from The Villum Foundation through a Villum Investigator Grant No. 25886. M. L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). F. J. and R. E. Z. acknowledge support from the Centre for Scientific Computing, Aarhus and the JKU scientific computing administration, Linz, respectively.","doi":"10.1103/PhysRevLett.131.053201","date_published":"2023-08-04T00:00:00Z","date_created":"2023-08-27T22:01:16Z","day":"04","publication":"Physical Review Letters","isi":1,"year":"2023","project":[{"name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"053201","title":"Nonadiabatic laser-induced alignment dynamics of molecules on a surface","author":[{"last_name":"Kranabetter","full_name":"Kranabetter, Lorenz","first_name":"Lorenz"},{"full_name":"Kristensen, Henrik H.","last_name":"Kristensen","first_name":"Henrik H."},{"last_name":"Ghazaryan","orcid":"0000-0001-9666-3543","full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"last_name":"Chatterley","full_name":"Chatterley, Adam S.","first_name":"Adam S."},{"first_name":"Paul","full_name":"Janssen, Paul","last_name":"Janssen"},{"full_name":"Jensen, Frank","last_name":"Jensen","first_name":"Frank"},{"full_name":"Zillich, Robert E.","last_name":"Zillich","first_name":"Robert E."},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail"},{"first_name":"Henrik","last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik"}],"external_id":{"arxiv":["2308.15247"],"isi":["001101784100001"],"pmid":["37595218"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Kranabetter, Lorenz, et al. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters, vol. 131, no. 5, 053201, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.053201.","ieee":"L. Kranabetter et al., “Nonadiabatic laser-induced alignment dynamics of molecules on a surface,” Physical Review Letters, vol. 131, no. 5. American Physical Society, 2023.","short":"L. Kranabetter, H.H. Kristensen, A. Ghazaryan, C.A. Schouder, A.S. Chatterley, P. Janssen, F. Jensen, R.E. Zillich, M. Lemeshko, H. Stapelfeldt, Physical Review Letters 131 (2023).","ama":"Kranabetter L, Kristensen HH, Ghazaryan A, et al. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 2023;131(5). doi:10.1103/PhysRevLett.131.053201","apa":"Kranabetter, L., Kristensen, H. H., Ghazaryan, A., Schouder, C. A., Chatterley, A. S., Janssen, P., … Stapelfeldt, H. (2023). Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.053201","chicago":"Kranabetter, Lorenz, Henrik H. Kristensen, Areg Ghazaryan, Constant A. Schouder, Adam S. Chatterley, Paul Janssen, Frank Jensen, Robert E. Zillich, Mikhail Lemeshko, and Henrik Stapelfeldt. “Nonadiabatic Laser-Induced Alignment Dynamics of Molecules on a Surface.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.053201.","ista":"Kranabetter L, Kristensen HH, Ghazaryan A, Schouder CA, Chatterley AS, Janssen P, Jensen F, Zillich RE, Lemeshko M, Stapelfeldt H. 2023. Nonadiabatic laser-induced alignment dynamics of molecules on a surface. Physical Review Letters. 131(5), 053201."}},{"publication_status":"published","publication_identifier":{"eissn":["1553-7374"],"issn":["1553-7366"]},"language":[{"iso":"eng"}],"file":[{"file_size":4458336,"date_updated":"2023-09-06T06:41:52Z","creator":"dernst","file_name":"2023_PloSPathogens_Koch.pdf","date_created":"2023-09-06T06:41:52Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14269","checksum":"47ca3bb54b27f28b05644be0ad064bc6"}],"volume":19,"issue":"8","acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Toscana virus is a major cause of arboviral disease in humans in the Mediterranean basin during summer. However, early virus-host cell interactions and entry mechanisms remain poorly characterized. Investigating iPSC-derived human neurons and cell lines, we found that virus binding to the cell surface was specific, and 50% of bound virions were endocytosed within 10 min. Virions entered Rab5a+ early endosomes and, subsequently, Rab7a+ and LAMP-1+ late endosomal compartments. Penetration required intact late endosomes and occurred within 30 min following internalization. Virus entry relied on vacuolar acidification, with an optimal pH for viral membrane fusion at pH 5.5. The pH threshold increased to 5.8 with longer pre-exposure of virions to the slightly acidic pH in early endosomes. Strikingly, the particles remained infectious after entering late endosomes with a pH below the fusion threshold. Overall, our study establishes Toscana virus as a late-penetrating virus and reveals an atypical use of vacuolar acidity by this virus to enter host cells."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 19","month":"08","date_updated":"2023-12-13T12:22:22Z","ddc":["570"],"department":[{"_id":"FlSc"}],"file_date_updated":"2023-09-06T06:41:52Z","_id":"14255","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","year":"2023","has_accepted_license":"1","isi":1,"publication":"PLoS Pathogens","day":"14","date_created":"2023-09-03T22:01:14Z","date_published":"2023-08-14T00:00:00Z","doi":"10.1371/journal.ppat.1011562","acknowledgement":"We acknowledge Elodie Chatre and the Imaging Platform Platim, SFR Biosciences, Lyon, as well as Vibor Laketa and the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) Heidelberg. The sand fly cell lines were supplied by the Tick Cell Biobank at the University of Liverpool. F.K.M.S. acknowledges support from the Scientific Service Units (SSUs) of ISTA through resources provided by the Electron Microscopy Facility (EMF).\r\nThis work was supported by CellNetworks Research Group funds and Deutsche Forschungsgemeinschaft (DFG) funding (LO-2338/3-1) and the Agence Nationale de la Recherche (ANR) funding (grant numbers ANR-21-CE11-0012 and ANR-22-CE15-0034), all awarded to P.-Y.L. This work was also supported by the LABEX ECOFECT (ANR-11-LABX-0048) of Université de Lyon (UDL), within the program “Investissements d’Avenir” (ANR-11-IDEX-0007) operated by the ANR and by the RESPOND program of the UDL (awarded to P.-Y.L) . C.A. was supported by the Chica and Heinz Schaller Research Group funds, NARSAD 2019 award, a Fritz Thyssen Research Grant, and the SFB1158-S02 grant. L.B-S. is supported by a United Kingdom Biotechnology and Biological Sciences Research Council grant (BB/P024270/1) and a Wellcome Trust grant (223743/Z/21/Z). F.K.M.S acknowledges support from the Austrian Science Fund (FWF, P31445). J.K. received a salary from the DFG (LO-2338/3-1) and then from the ANR (ANR-11-LABX-0048). The salary of Z.M.U. was partially covered by the DFG (LO-2338/3-1). S.K. received a salary from the DFG (SFB1129). We are grateful to the Chinese Scholarship Council (CSC; 201904910701), DAAD/ANID (57451854/62180003), the Rufus A. Kellogg fellowship program (Amherst College, Massachusetts, USA) for awarding fellowships to Q.X., J.C., and H.A.A., respectively.","oa":1,"publisher":"Public Library of Science","quality_controlled":"1","citation":{"chicago":"Koch, Jana, Qilin Xin, Martin Obr, Alicia Schäfer, Nina Rolfs, Holda A. Anagho, Aiste Kudulyte, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens. Public Library of Science, 2023. https://doi.org/10.1371/journal.ppat.1011562.","ista":"Koch J, Xin Q, Obr M, Schäfer A, Rolfs N, Anagho HA, Kudulyte A, Woltereck L, Kummer S, Campos J, Uckeley ZM, Bell-Sakyi L, Kräusslich HG, Schur FK, Acuna C, Lozach PY. 2023. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 19(8), e1011562.","mla":"Koch, Jana, et al. “The Phenuivirus Toscana Virus Makes an Atypical Use of Vacuolar Acidity to Enter Host Cells.” PLoS Pathogens, vol. 19, no. 8, e1011562, Public Library of Science, 2023, doi:10.1371/journal.ppat.1011562.","short":"J. Koch, Q. Xin, M. Obr, A. Schäfer, N. Rolfs, H.A. Anagho, A. Kudulyte, L. Woltereck, S. Kummer, J. Campos, Z.M. Uckeley, L. Bell-Sakyi, H.G. Kräusslich, F.K. Schur, C. Acuna, P.Y. Lozach, PLoS Pathogens 19 (2023).","ieee":"J. Koch et al., “The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells,” PLoS Pathogens, vol. 19, no. 8. Public Library of Science, 2023.","apa":"Koch, J., Xin, Q., Obr, M., Schäfer, A., Rolfs, N., Anagho, H. A., … Lozach, P. Y. (2023). The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. Public Library of Science. https://doi.org/10.1371/journal.ppat.1011562","ama":"Koch J, Xin Q, Obr M, et al. The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells. PLoS Pathogens. 2023;19(8). doi:10.1371/journal.ppat.1011562"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37578957"],"isi":["001050846300004"]},"article_processing_charge":"Yes","author":[{"full_name":"Koch, Jana","last_name":"Koch","first_name":"Jana"},{"last_name":"Xin","full_name":"Xin, Qilin","first_name":"Qilin"},{"id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Obr","full_name":"Obr, Martin","orcid":"0000-0003-1756-6564"},{"first_name":"Alicia","full_name":"Schäfer, Alicia","last_name":"Schäfer"},{"first_name":"Nina","last_name":"Rolfs","full_name":"Rolfs, Nina"},{"first_name":"Holda A.","last_name":"Anagho","full_name":"Anagho, Holda A."},{"full_name":"Kudulyte, Aiste","last_name":"Kudulyte","first_name":"Aiste"},{"last_name":"Woltereck","full_name":"Woltereck, Lea","first_name":"Lea"},{"last_name":"Kummer","full_name":"Kummer, Susann","first_name":"Susann"},{"full_name":"Campos, Joaquin","last_name":"Campos","first_name":"Joaquin"},{"last_name":"Uckeley","full_name":"Uckeley, Zina M.","first_name":"Zina M."},{"last_name":"Bell-Sakyi","full_name":"Bell-Sakyi, Lesley","first_name":"Lesley"},{"first_name":"Hans Georg","full_name":"Kräusslich, Hans Georg","last_name":"Kräusslich"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian Km","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian Km"},{"last_name":"Acuna","full_name":"Acuna, Claudio","first_name":"Claudio"},{"first_name":"Pierre Yves","full_name":"Lozach, Pierre Yves","last_name":"Lozach"}],"title":"The phenuivirus Toscana virus makes an atypical use of vacuolar acidity to enter host cells","article_number":"e1011562","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445"}]},{"isi":1,"has_accepted_license":"1","year":"2023","day":"01","publication":"Nature Plants","page":"1500-1513","date_published":"2023-09-01T00:00:00Z","doi":"10.1038/s41477-023-01478-x","date_created":"2023-09-15T09:56:01Z","acknowledgement":"We thank D. Weijers, C. Schwechheimer and R. Offringa for generous sharing of published and unpublished materials and P. Masson for advice on the use of the ARL2 promoter. We are grateful to M. Del Bianco and O. Leyser for critical reading of the manuscript. This work was supported by the BBSRC (grants BB/N010124/1 and BB/R000859/1 to S.K.), the Gatsby Charitable Foundation and the Leverhulme Trust (RPG-2018-137 to S.K.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"citation":{"mla":"Roychoudhry, S., et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants, vol. 9, Springer Nature, 2023, pp. 1500–13, doi:10.1038/s41477-023-01478-x.","apa":"Roychoudhry, S., Sageman-Furnas, K., Wolverton, C., Grones, P., Tan, S., Molnar, G., … Kepinski, S. (2023). Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-023-01478-x","ama":"Roychoudhry S, Sageman-Furnas K, Wolverton C, et al. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 2023;9:1500-1513. doi:10.1038/s41477-023-01478-x","ieee":"S. Roychoudhry et al., “Antigravitropic PIN polarization maintains non-vertical growth in lateral roots,” Nature Plants, vol. 9. Springer Nature, pp. 1500–1513, 2023.","short":"S. Roychoudhry, K. Sageman-Furnas, C. Wolverton, P. Grones, S. Tan, G. Molnar, M. De Angelis, H. Goodman, N. Capstaff, L. JPB, J. Mullen, R. Hangarter, J. Friml, S. Kepinski, Nature Plants 9 (2023) 1500–1513.","chicago":"Roychoudhry, S, K Sageman-Furnas, C Wolverton, Peter Grones, Shutang Tan, Gergely Molnar, M De Angelis, et al. “Antigravitropic PIN Polarization Maintains Non-Vertical Growth in Lateral Roots.” Nature Plants. Springer Nature, 2023. https://doi.org/10.1038/s41477-023-01478-x.","ista":"Roychoudhry S, Sageman-Furnas K, Wolverton C, Grones P, Tan S, Molnar G, De Angelis M, Goodman H, Capstaff N, JPB L, Mullen J, Hangarter R, Friml J, Kepinski S. 2023. Antigravitropic PIN polarization maintains non-vertical growth in lateral roots. Nature Plants. 9, 1500–1513."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"S","last_name":"Roychoudhry","full_name":"Roychoudhry, S"},{"first_name":"K","full_name":"Sageman-Furnas, K","last_name":"Sageman-Furnas"},{"last_name":"Wolverton","full_name":"Wolverton, C","first_name":"C"},{"id":"399876EC-F248-11E8-B48F-1D18A9856A87","first_name":"Peter","full_name":"Grones, Peter","last_name":"Grones"},{"last_name":"Tan","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","first_name":"Shutang"},{"first_name":"Gergely","id":"34F1AF46-F248-11E8-B48F-1D18A9856A87","full_name":"Molnar, Gergely","last_name":"Molnar"},{"last_name":"De Angelis","full_name":"De Angelis, M","first_name":"M"},{"last_name":"Goodman","full_name":"Goodman, HL","first_name":"HL"},{"first_name":"N","last_name":"Capstaff","full_name":"Capstaff, N"},{"first_name":"Lloyd","last_name":"JPB","full_name":"JPB, Lloyd"},{"first_name":"J","last_name":"Mullen","full_name":"Mullen, J"},{"first_name":"R","full_name":"Hangarter, R","last_name":"Hangarter"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"S","full_name":"Kepinski, S","last_name":"Kepinski"}],"external_id":{"isi":["001069238800014"],"pmid":["37666965"]},"article_processing_charge":"Yes (in subscription journal)","title":"Antigravitropic PIN polarization maintains non-vertical growth in lateral roots","publication_identifier":{"issn":["2055-0278"]},"publication_status":"published","file":[{"date_created":"2023-09-20T10:51:31Z","file_name":"2023_NaturePlants_Roychoudhry.pdf","date_updated":"2023-09-20T10:51:31Z","file_size":9647103,"creator":"dernst","checksum":"3d6d5d5abb937c14a5f6f0afba3b8624","file_id":"14351","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"volume":9,"abstract":[{"text":"Lateral roots are typically maintained at non-vertical angles with respect to gravity. These gravitropic setpoint angles are intriguing because their maintenance requires that roots are able to effect growth response both with and against the gravity vector, a phenomenon previously attributed to gravitropism acting against an antigravitropic offset mechanism. Here we show how the components mediating gravitropism in the vertical primary root—PINs and phosphatases acting upon them—are reconfigured in their regulation such that lateral root growth at a range of angles can be maintained. We show that the ability of Arabidopsis lateral roots to bend both downward and upward requires the generation of auxin asymmetries and is driven by angle-dependent variation in downward gravitropic auxin flux acting against angle-independent upward, antigravitropic flux. Further, we demonstrate a symmetry in auxin distribution in lateral roots at gravitropic setpoint angle that can be traced back to a net, balanced polarization of PIN3 and PIN7 auxin transporters in the columella. These auxin fluxes are shifted by altering PIN protein phosphoregulation in the columella, either by introducing PIN3 phosphovariant versions or via manipulation of levels of the phosphatase subunit PP2A/RCN1. Finally, we show that auxin, in addition to driving lateral root directional growth, acts within the lateral root columella to induce more vertical growth by increasing RCN1 levels, causing a downward shift in PIN3 localization, thereby diminishing the magnitude of the upward, antigravitropic auxin flux.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"month":"09","intvolume":" 9","date_updated":"2023-12-13T12:23:49Z","ddc":["580"],"department":[{"_id":"JiFr"}],"file_date_updated":"2023-09-20T10:51:31Z","_id":"14339","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14363","file_date_updated":"2023-11-07T08:53:21Z","department":[{"_id":"SaSi"}],"ddc":["570"],"date_updated":"2023-12-13T12:27:30Z","intvolume":" 26","month":"10","scopus_import":"1","pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"abstract":[{"text":"Mitochondrial networks remodel their connectivity, content, and subcellular localization to support optimized energy production in conditions of increased environmental or cellular stress. Microglia rely on mitochondria to respond to these stressors, however our knowledge about mitochondrial networks and their adaptations in microglia in vivo is limited. Here, we generate a mouse model that selectively labels mitochondria in microglia. We identify that mitochondrial networks are more fragmented with increased content and perinuclear localization in vitro vs. in vivo. Mitochondrial networks adapt similarly in microglia closest to the injury site after optic nerve crush. Preventing microglial UCP2 increase after injury by selective knockout induces cellular stress. This results in mitochondrial hyperfusion in male microglia, a phenotype absent in females due to circulating estrogens. Our results establish the foundation for mitochondrial network analysis of microglia in vivo, emphasizing the importance of mitochondrial-based sex effects of microglia in other pathologies.","lang":"eng"}],"volume":26,"issue":"10","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"be1a560efdd96d20712311f4fc54aac2","file_id":"14497","success":1,"creator":"dernst","date_updated":"2023-11-07T08:53:21Z","file_size":8197935,"date_created":"2023-11-07T08:53:21Z","file_name":"2023_iScience_Maes.pdf"}],"publication_status":"published","publication_identifier":{"eissn":["2589-0042"]},"article_number":"107780","title":"Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout","article_processing_charge":"Yes","external_id":{"pmid":["37731609"],"isi":["001080403500001"]},"author":[{"first_name":"Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","full_name":"Maes, Margaret E","last_name":"Maes"},{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"},{"first_name":"Florianne E","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","last_name":"Schoot Uiterkamp"},{"first_name":"Felix","last_name":"Sternberg","full_name":"Sternberg, Felix"},{"last_name":"Venturino","full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elena E.","last_name":"Pohl","full_name":"Pohl, Elena E."},{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","first_name":"Sandra","last_name":"Siegert","full_name":"Siegert, Sandra","orcid":"0000-0001-8635-0877"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Maes, M. E., Colombo, G., Schoot Uiterkamp, F. E., Sternberg, F., Venturino, A., Pohl, E. E., & Siegert, S. (2023). Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107780","ama":"Maes ME, Colombo G, Schoot Uiterkamp FE, et al. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 2023;26(10). doi:10.1016/j.isci.2023.107780","short":"M.E. Maes, G. Colombo, F.E. Schoot Uiterkamp, F. Sternberg, A. Venturino, E.E. Pohl, S. Siegert, IScience 26 (2023).","ieee":"M. E. Maes et al., “Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout,” iScience, vol. 26, no. 10. Elsevier, 2023.","mla":"Maes, Margaret E., et al. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience, vol. 26, no. 10, 107780, Elsevier, 2023, doi:10.1016/j.isci.2023.107780.","ista":"Maes ME, Colombo G, Schoot Uiterkamp FE, Sternberg F, Venturino A, Pohl EE, Siegert S. 2023. Mitochondrial network adaptations of microglia reveal sex-specific stress response after injury and UCP2 knockout. iScience. 26(10), 107780.","chicago":"Maes, Margaret E, Gloria Colombo, Florianne E Schoot Uiterkamp, Felix Sternberg, Alessandro Venturino, Elena E. Pohl, and Sandra Siegert. “Mitochondrial Network Adaptations of Microglia Reveal Sex-Specific Stress Response after Injury and UCP2 Knockout.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107780."},"oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"We thank the Scientific Service Units (SSU) of ISTA through resources provided by the Imaging and Optics Facility (IOF), the Lab Support Facility (LSF), and the Pre-Clinical Facility (PCF) team, specifically Sonja Haslinger and Michael Schunn for excellent mouse colony management and support. This research was supported by the FWF Sonderforschungsbereich F83 (to E.E.P). We thank Bálint Nagy, Ryan John A. Cubero, Marco Benevento and all members of the Siegert group for constant feedback on the project and article.","date_created":"2023-09-24T22:01:11Z","doi":"10.1016/j.isci.2023.107780","date_published":"2023-10-20T00:00:00Z","publication":"iScience","day":"20","year":"2023","has_accepted_license":"1","isi":1},{"article_number":"e74","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Cipolloni, Giorgio, László Erdös, Sven Joscha Henheik, and Oleksii Kolupaiev. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma. Cambridge University Press, 2023. https://doi.org/10.1017/fms.2023.70.","ista":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. 2023. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 11, e74.","mla":"Cipolloni, Giorgio, et al. “Gaussian Fluctuations in the Equipartition Principle for Wigner Matrices.” Forum of Mathematics, Sigma, vol. 11, e74, Cambridge University Press, 2023, doi:10.1017/fms.2023.70.","apa":"Cipolloni, G., Erdös, L., Henheik, S. J., & Kolupaiev, O. (2023). Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2023.70","ama":"Cipolloni G, Erdös L, Henheik SJ, Kolupaiev O. Gaussian fluctuations in the equipartition principle for Wigner matrices. Forum of Mathematics, Sigma. 2023;11. doi:10.1017/fms.2023.70","short":"G. Cipolloni, L. Erdös, S.J. Henheik, O. Kolupaiev, Forum of Mathematics, Sigma 11 (2023).","ieee":"G. Cipolloni, L. Erdös, S. J. Henheik, and O. Kolupaiev, “Gaussian fluctuations in the equipartition principle for Wigner matrices,” Forum of Mathematics, Sigma, vol. 11. Cambridge University Press, 2023."},"title":"Gaussian fluctuations in the equipartition principle for Wigner matrices","external_id":{"isi":["001051980200001"],"arxiv":["2301.05181"]},"article_processing_charge":"Yes","author":[{"last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgio"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603"},{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha","last_name":"Henheik","full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X"},{"id":"149b70d4-896a-11ed-bdf8-8c63fd44ca61","first_name":"Oleksii","full_name":"Kolupaiev, Oleksii","last_name":"Kolupaiev"}],"acknowledgement":"G.C. and L.E. gratefully acknowledge many discussions with Dominik Schröder at the preliminary stage of this project, especially his essential contribution to identify the correct generalisation of traceless observables to the deformed Wigner ensembles.\r\nL.E. and J.H. acknowledges support by ERC Advanced Grant ‘RMTBeyond’ No. 101020331.","oa":1,"publisher":"Cambridge University Press","quality_controlled":"1","publication":"Forum of Mathematics, Sigma","day":"23","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-09-17T22:01:09Z","date_published":"2023-08-23T00:00:00Z","doi":"10.1017/fms.2023.70","_id":"14343","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["510"],"date_updated":"2023-12-13T12:24:23Z","file_date_updated":"2023-09-20T11:09:35Z","department":[{"_id":"LaEr"},{"_id":"GradSch"}],"oa_version":"Published Version","abstract":[{"text":"The total energy of an eigenstate in a composite quantum system tends to be distributed equally among its constituents. We identify the quantum fluctuation around this equipartition principle in the simplest disordered quantum system consisting of linear combinations of Wigner matrices. As our main ingredient, we prove the Eigenstate Thermalisation Hypothesis and Gaussian fluctuation for general quadratic forms of the bulk eigenvectors of Wigner matrices with an arbitrary deformation.","lang":"eng"}],"intvolume":" 11","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":852652,"date_updated":"2023-09-20T11:09:35Z","file_name":"2023_ForumMathematics_Cipolloni.pdf","date_created":"2023-09-20T11:09:35Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"eb747420e6a88a7796fa934151957676","file_id":"14352"}],"publication_status":"published","publication_identifier":{"eissn":["2050-5094"]},"ec_funded":1,"volume":11},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"ec_funded":1,"issue":"4","volume":52,"related_material":{"record":[{"id":"6676","status":"public","relation":"earlier_version"}]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We introduce extension-based proofs, a class of impossibility proofs that includes valency arguments. They are modelled as an interaction between a prover and a protocol. Using proofs based on combinatorial topology, it has been shown that it is impossible to deterministically solve -set agreement among processes or approximate agreement on a cycle of length 4 among processes in a wait-free manner in asynchronous models where processes communicate using objects that can be constructed from shared registers. However, it was unknown whether proofs based on simpler techniques were possible. We show that these impossibility results cannot be obtained by extension-based proofs in the iterated snapshot model and, hence, extension-based proofs are limited in power."}],"intvolume":" 52","month":"07","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.01421"}],"scopus_import":"1","date_updated":"2023-12-13T12:28:29Z","department":[{"_id":"DaAl"}],"_id":"14364","status":"public","type":"journal_article","article_type":"original","publication":"SIAM Journal on Computing","day":"25","year":"2023","isi":1,"date_created":"2023-09-24T22:01:11Z","doi":"10.1137/20M1375851","date_published":"2023-07-25T00:00:00Z","page":"913-944","acknowledgement":"We would like to thank Valerie King, Toniann Pitassi, and Michael Saks for helpful discussions and Shi Hao Liu for his useful feedback.\r\nThis research was supported by the Natural Science and Engineering Research Council of Canada under grants RGPIN-2015-05080 and RGPIN-2020-04178, a postgraduate scholarship, and a postdoctoral fellowship; a University of Toronto postdoctoral fellowship; the National Science Foundation under grants CCF-1217921, CCF-1301926, CCF-1637385, CCF-1650596, and IIS-1447786; the U.S. Department of Energy under grant ER26116/DE-SC0008923; the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme grant agreement 805223 ScaleML; and the Oracle and Intel corporations. Some of the work on this paper was done while Faith Ellen was visiting IST Austria.","oa":1,"publisher":"Society for Industrial and Applied Mathematics","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alistarh, Dan-Adrian, James Aspnes, Faith Ellen, Rati Gelashvili, and Leqi Zhu. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/20M1375851.","ista":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. 2023. Why extension-based proofs fail. SIAM Journal on Computing. 52(4), 913–944.","mla":"Alistarh, Dan-Adrian, et al. “Why Extension-Based Proofs Fail.” SIAM Journal on Computing, vol. 52, no. 4, Society for Industrial and Applied Mathematics, 2023, pp. 913–44, doi:10.1137/20M1375851.","short":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, L. Zhu, SIAM Journal on Computing 52 (2023) 913–944.","ieee":"D.-A. Alistarh, J. Aspnes, F. Ellen, R. Gelashvili, and L. Zhu, “Why extension-based proofs fail,” SIAM Journal on Computing, vol. 52, no. 4. Society for Industrial and Applied Mathematics, pp. 913–944, 2023.","ama":"Alistarh D-A, Aspnes J, Ellen F, Gelashvili R, Zhu L. Why extension-based proofs fail. SIAM Journal on Computing. 2023;52(4):913-944. doi:10.1137/20M1375851","apa":"Alistarh, D.-A., Aspnes, J., Ellen, F., Gelashvili, R., & Zhu, L. (2023). Why extension-based proofs fail. SIAM Journal on Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/20M1375851"},"title":"Why extension-based proofs fail","article_processing_charge":"No","external_id":{"isi":["001082972300004"],"arxiv":["1811.01421"]},"author":[{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"James","full_name":"Aspnes, James","last_name":"Aspnes"},{"last_name":"Ellen","full_name":"Ellen, Faith","first_name":"Faith"},{"full_name":"Gelashvili, Rati","last_name":"Gelashvili","first_name":"Rati"},{"last_name":"Zhu","full_name":"Zhu, Leqi","id":"a2117c59-cee4-11ed-b9d0-874ecf0f8ac5","first_name":"Leqi"}],"project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}]},{"oa_version":"Published Version","abstract":[{"text":"For a locally finite set in R2, the order-k Brillouin tessellations form an infinite sequence of convex face-to-face tilings of the plane. If the set is coarsely dense and generic, then the corresponding infinite sequences of minimum and maximum angles are both monotonic in k. As an example, a stationary Poisson point process in R2 is locally finite, coarsely dense, and generic with probability one. For such a set, the distributions of angles in the Voronoi tessellations, Delaunay mosaics, and Brillouin tessellations are independent of the order and can be derived from the formula for angles in order-1 Delaunay mosaics given by Miles (Math. Biosci. 6, 85–127 (1970)).","lang":"eng"}],"month":"09","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00454-023-00566-1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"publication_status":"epub_ahead","ec_funded":1,"_id":"14345","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-12-13T12:25:06Z","department":[{"_id":"HeEd"}],"acknowledgement":"Work by all authors but A. Garber is supported by the European Research Council (ERC), Grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), Grant No. I 02979-N35. Work by A. Garber is partially supported by the Alexander von Humboldt Foundation.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"07","publication":"Discrete and Computational Geometry","isi":1,"year":"2023","doi":"10.1007/s00454-023-00566-1","date_published":"2023-09-07T00:00:00Z","date_created":"2023-09-17T22:01:10Z","project":[{"grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Edelsbrunner, Herbert, et al. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry, Springer Nature, 2023, doi:10.1007/s00454-023-00566-1.","apa":"Edelsbrunner, H., Garber, A., Ghafari, M., Heiss, T., & Saghafian, M. (2023). On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00566-1","ama":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry. 2023. doi:10.1007/s00454-023-00566-1","ieee":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, and M. Saghafian, “On angles in higher order Brillouin tessellations and related tilings in the plane,” Discrete and Computational Geometry. Springer Nature, 2023.","short":"H. Edelsbrunner, A. Garber, M. Ghafari, T. Heiss, M. Saghafian, Discrete and Computational Geometry (2023).","chicago":"Edelsbrunner, Herbert, Alexey Garber, Mohadese Ghafari, Teresa Heiss, and Morteza Saghafian. “On Angles in Higher Order Brillouin Tessellations and Related Tilings in the Plane.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00566-1.","ista":"Edelsbrunner H, Garber A, Ghafari M, Heiss T, Saghafian M. 2023. On angles in higher order Brillouin tessellations and related tilings in the plane. Discrete and Computational Geometry."},"title":"On angles in higher order Brillouin tessellations and related tilings in the plane","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Garber, Alexey","last_name":"Garber","first_name":"Alexey"},{"last_name":"Ghafari","full_name":"Ghafari, Mohadese","first_name":"Mohadese"},{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","last_name":"Heiss","full_name":"Heiss, Teresa","orcid":"0000-0002-1780-2689"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"external_id":{"isi":["001060727600004"],"arxiv":["2204.01076"]},"article_processing_charge":"Yes (via OA deal)"},{"acknowledgement":"We thank Dr. Kari Alitalo (University of Helsinki and Wihuri Research Institute) for critical reading of the manuscript, providing Vegfc+/− and Clp24ΔEC mouse strains and for hosting K.V.’s Academy of Finland postdoctoral researcher period (2015–2018). We thank Dr. Sara Wickström (University of Helsinki and Wihuri Research Institute) for providing Sox9:Egfp mouse\r\nstrain and the discussions. We thank Maija Atuegwu and Tapio Tainola for technical assistance. This work received funding from the Academy of Finland (K.V., 315710), Sigrid Juselius Foundation (K.V.), University of Helsinki (K.V.), Wihuri Research Institute (K.V.), the ERC under the European Union’s Horizon 2020 research and innovation program (grant agreement\r\nNo. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.). Part of the work was carried out with the support of HiLIFE Laboratory Animal Centre Core Facility, University of Helsinki, Finland. Imaging was performed at the Biomedicum Imaging Unit, Helsinki University, Helsinki, Finland, with the support of Biocenter Finland. The AAVpreparations were produced at the Helsinki Virus (HelVi) Core.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"21","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2023","doi":"10.1038/s41467-023-41456-7","date_published":"2023-09-21T00:00:00Z","date_created":"2023-10-01T22:01:13Z","article_number":"5878","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ucar, Mehmet C, Edouard B Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, and Kari Vaahtomeri. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41456-7.","ista":"Ucar MC, Hannezo EB, Tiilikainen E, Liaqat I, Jakobsson E, Nurmi H, Vaahtomeri K. 2023. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 14, 5878.","mla":"Ucar, Mehmet C., et al. “Self-Organized and Directed Branching Results in Optimal Coverage in Developing Dermal Lymphatic Networks.” Nature Communications, vol. 14, 5878, Springer Nature, 2023, doi:10.1038/s41467-023-41456-7.","apa":"Ucar, M. C., Hannezo, E. B., Tiilikainen, E., Liaqat, I., Jakobsson, E., Nurmi, H., & Vaahtomeri, K. (2023). Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41456-7","ama":"Ucar MC, Hannezo EB, Tiilikainen E, et al. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks. Nature Communications. 2023;14. doi:10.1038/s41467-023-41456-7","short":"M.C. Ucar, E.B. Hannezo, E. Tiilikainen, I. Liaqat, E. Jakobsson, H. Nurmi, K. Vaahtomeri, Nature Communications 14 (2023).","ieee":"M. C. Ucar et al., “Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks,” Nature Communications, vol. 14. Springer Nature, 2023."},"title":"Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Emmi","last_name":"Tiilikainen","full_name":"Tiilikainen, Emmi"},{"full_name":"Liaqat, Inam","last_name":"Liaqat","first_name":"Inam"},{"first_name":"Emma","full_name":"Jakobsson, Emma","last_name":"Jakobsson"},{"first_name":"Harri","full_name":"Nurmi, Harri","last_name":"Nurmi"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"}],"article_processing_charge":"Yes","external_id":{"pmid":["37735168"],"isi":["001075884500007"]},"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization."}],"month":"09","intvolume":" 14","scopus_import":"1","file":[{"file_name":"2023_NatureComm_Ucar.pdf","date_created":"2023-10-03T07:46:36Z","creator":"dernst","file_size":8143264,"date_updated":"2023-10-03T07:46:36Z","success":1,"file_id":"14384","checksum":"4fe5423403f2531753bcd9e0fea48e05","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","volume":14,"ec_funded":1,"_id":"14378","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["570"],"date_updated":"2023-12-13T12:31:05Z","file_date_updated":"2023-10-03T07:46:36Z","department":[{"_id":"EdHa"}]},{"year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"13","date_created":"2023-09-24T22:01:10Z","date_published":"2023-09-13T00:00:00Z","doi":"10.1038/s41467-023-41432-1","acknowledgement":"We thank K. O’Keeffe, E. Hannezo, P. Devreotes, C. Dessalles, and E. Martens for discussion and/or critical reading of the manuscript; the Bioimaging Facility of ISTA for excellent support, as well as the Life Science Facility and the Miba Machine Shop of ISTA. This work was supported by the European Research Council (ERC StG 281556 and CoG 724373) to M.S.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"ista":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. 2023. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 14, 5633.","chicago":"Riedl, Michael, Isabelle D Mayer, Jack Merrin, Michael K Sixt, and Björn Hof. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41432-1.","ama":"Riedl M, Mayer ID, Merrin J, Sixt MK, Hof B. Synchronization in collectively moving inanimate and living active matter. Nature Communications. 2023;14. doi:10.1038/s41467-023-41432-1","apa":"Riedl, M., Mayer, I. D., Merrin, J., Sixt, M. K., & Hof, B. (2023). Synchronization in collectively moving inanimate and living active matter. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41432-1","short":"M. Riedl, I.D. Mayer, J. Merrin, M.K. Sixt, B. Hof, Nature Communications 14 (2023).","ieee":"M. Riedl, I. D. Mayer, J. Merrin, M. K. Sixt, and B. Hof, “Synchronization in collectively moving inanimate and living active matter,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Riedl, Michael, et al. “Synchronization in Collectively Moving Inanimate and Living Active Matter.” Nature Communications, vol. 14, 5633, Springer Nature, 2023, doi:10.1038/s41467-023-41432-1."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"pmid":["37704595"],"isi":["001087583700030"]},"author":[{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl"},{"first_name":"Isabelle D","id":"61763940-15b2-11ec-abd3-cfaddfbc66b4","last_name":"Mayer","full_name":"Mayer, Isabelle D"},{"last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"},{"first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"}],"title":"Synchronization in collectively moving inanimate and living active matter","article_number":"5633","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes"},{"call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"checksum":"82d2d4ad736cc8493db8ce45cd313f7b","file_id":"14366","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2023-09-25T08:32:37Z","file_name":"2023_NatureComm_Riedl.pdf","creator":"dernst","date_updated":"2023-09-25T08:32:37Z","file_size":2317272}],"ec_funded":1,"volume":14,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Whether one considers swarming insects, flocking birds, or bacterial colonies, collective motion arises from the coordination of individuals and entails the adjustment of their respective velocities. In particular, in close confinements, such as those encountered by dense cell populations during development or regeneration, collective migration can only arise coordinately. Yet, how individuals unify their velocities is often not understood. Focusing on a finite number of cells in circular confinements, we identify waves of polymerizing actin that function as a pacemaker governing the speed of individual cells. We show that the onset of collective motion coincides with the synchronization of the wave nucleation frequencies across the population. Employing a simpler and more readily accessible mechanical model system of active spheres, we identify the synchronization of the individuals’ internal oscillators as one of the essential requirements to reach the corresponding collective state. The mechanical ‘toy’ experiment illustrates that the global synchronous state is achieved by nearest neighbor coupling. We suggest by analogy that local coupling and the synchronization of actin waves are essential for the emergent, self-organized motion of cell collectives."}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 14","month":"09","date_updated":"2023-12-13T12:29:41Z","ddc":["530","570"],"file_date_updated":"2023-09-25T08:32:37Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"BjHo"}],"_id":"14361","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"oa_version":"Published Version","abstract":[{"text":"Only recently has it been possible to construct a self-adjoint Hamiltonian that involves the creation of Dirac particles at a point source in 3d space. Its definition makes use of an interior-boundary condition. Here, we develop for this Hamiltonian a corresponding theory of the Bohmian configuration. That is, we (non-rigorously) construct a Markov jump process $(Q_t)_{t\\in\\mathbb{R}}$ in the configuration space of a variable number of particles that is $|\\psi_t|^2$-distributed at every time t and follows Bohmian trajectories between the jumps. The jumps correspond to particle creation or annihilation events and occur either to or from a configuration with a particle located at the source. The process is the natural analog of Bell's jump process, and a central piece in its construction is the determination of the rate of particle creation. The construction requires an analysis of the asymptotic behavior of the Bohmian trajectories near the source. We find that the particle reaches the source with radial speed 0, but orbits around the source infinitely many times in finite time before absorption (or after emission).","lang":"eng"}],"month":"10","intvolume":" 56","scopus_import":"1","file":[{"date_updated":"2023-10-16T07:07:24Z","file_size":721399,"creator":"dernst","date_created":"2023-10-16T07:07:24Z","file_name":"2023_JourPhysics_Henheik.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14429","checksum":"5b68de147dd4c608b71a6e0e844d2ce9","success":1}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1751-8113"],"eissn":["1751-8121"]},"publication_status":"published","volume":56,"issue":"44","ec_funded":1,"_id":"14421","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["510"],"date_updated":"2023-12-13T13:01:25Z","department":[{"_id":"GradSch"},{"_id":"LaEr"}],"file_date_updated":"2023-10-16T07:07:24Z","acknowledgement":"J H gratefully acknowledges partial financial support by the ERC Advanced Grant 'RMTBeyond' No. 101020331.","publisher":"IOP Publishing","quality_controlled":"1","oa":1,"day":"11","publication":"Journal of Physics A: Mathematical and Theoretical","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1088/1751-8121/acfe62","date_published":"2023-10-11T00:00:00Z","date_created":"2023-10-12T12:42:53Z","article_number":"445201","project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical. IOP Publishing, 2023. https://doi.org/10.1088/1751-8121/acfe62.","ista":"Henheik SJ, Tumulka R. 2023. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 56(44), 445201.","mla":"Henheik, Sven Joscha, and Roderich Tumulka. “Creation Rate of Dirac Particles at a Point Source.” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44, 445201, IOP Publishing, 2023, doi:10.1088/1751-8121/acfe62.","short":"S.J. Henheik, R. Tumulka, Journal of Physics A: Mathematical and Theoretical 56 (2023).","ieee":"S. J. Henheik and R. Tumulka, “Creation rate of Dirac particles at a point source,” Journal of Physics A: Mathematical and Theoretical, vol. 56, no. 44. IOP Publishing, 2023.","apa":"Henheik, S. J., & Tumulka, R. (2023). Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. IOP Publishing. https://doi.org/10.1088/1751-8121/acfe62","ama":"Henheik SJ, Tumulka R. Creation rate of Dirac particles at a point source. Journal of Physics A: Mathematical and Theoretical. 2023;56(44). doi:10.1088/1751-8121/acfe62"},"title":"Creation rate of Dirac particles at a point source","author":[{"full_name":"Henheik, Sven Joscha","orcid":"0000-0003-1106-327X","last_name":"Henheik","id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","first_name":"Sven Joscha"},{"first_name":"Roderich","full_name":"Tumulka, Roderich","last_name":"Tumulka"}],"external_id":{"arxiv":["2211.16606"],"isi":["001080908000001"]},"article_processing_charge":"Yes (via OA deal)"},{"acknowledgement":"We thank Daniel Hausmann and Nir Piterman for their valuable comments on an earlier version of the manuscript of our other paper [22] where we present, among other things, the parity fixpoint for 2 1/2-player games (for a slightly more general class of games) with a different and indirect proof of correctness. Based on their comments we observed that, unlike the other fixpoints that we present in [22], the parity fixpoint does not follow the exact same structure as its counterpart for 2-player games, which we also use int his paper.\r\nWe also thank Thejaswini Raghavan for observing that our symbolic parity fixpoint algorithm can be solved in quasi-polynomial time using recent improved algorithms for solving \r\n-calculus expressions. This significantly improved the complexity bounds of our algorithm in this paper.\r\nThe work of R. Majumdar and A.-K. Schmuck are partially supported by DFG, Germany project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG, Germany project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047.","oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Nonlinear Analysis: Hybrid Systems","day":"27","year":"2023","isi":1,"date_created":"2023-10-08T22:01:15Z","doi":"10.1016/j.nahs.2023.101430","date_published":"2023-09-27T00:00:00Z","article_number":"101430","project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. 2023. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 51, 101430.","chicago":"Majumdar, Rupak, Kaushik Mallik, Anne Kathrin Schmuck, and Sadegh Soudjani. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems. Elsevier, 2023. https://doi.org/10.1016/j.nahs.2023.101430.","apa":"Majumdar, R., Mallik, K., Schmuck, A. K., & Soudjani, S. (2023). Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. Elsevier. https://doi.org/10.1016/j.nahs.2023.101430","ama":"Majumdar R, Mallik K, Schmuck AK, Soudjani S. Symbolic control for stochastic systems via finite parity games. Nonlinear Analysis: Hybrid Systems. 2023;51. doi:10.1016/j.nahs.2023.101430","ieee":"R. Majumdar, K. Mallik, A. K. Schmuck, and S. Soudjani, “Symbolic control for stochastic systems via finite parity games,” Nonlinear Analysis: Hybrid Systems, vol. 51. Elsevier, 2023.","short":"R. Majumdar, K. Mallik, A.K. Schmuck, S. Soudjani, Nonlinear Analysis: Hybrid Systems 51 (2023).","mla":"Majumdar, Rupak, et al. “Symbolic Control for Stochastic Systems via Finite Parity Games.” Nonlinear Analysis: Hybrid Systems, vol. 51, 101430, Elsevier, 2023, doi:10.1016/j.nahs.2023.101430."},"title":"Symbolic control for stochastic systems via finite parity games","external_id":{"arxiv":["2101.00834"],"isi":["001093188100001"]},"article_processing_charge":"No","author":[{"first_name":"Rupak","last_name":"Majumdar","full_name":"Majumdar, Rupak"},{"orcid":"0000-0001-9864-7475","full_name":"Mallik, Kaushik","last_name":"Mallik","first_name":"Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598"},{"first_name":"Anne Kathrin","full_name":"Schmuck, Anne Kathrin","last_name":"Schmuck"},{"full_name":"Soudjani, Sadegh","last_name":"Soudjani","first_name":"Sadegh"}],"oa_version":"Published Version","abstract":[{"text":"We consider the problem of computing the maximal probability of satisfying an \r\n-regular specification for stochastic, continuous-state, nonlinear systems evolving in discrete time. The problem reduces, after automata-theoretic constructions, to finding the maximal probability of satisfying a parity condition on a (possibly hybrid) state space. While characterizing the exact satisfaction probability is open, we show that a lower bound on this probability can be obtained by (I) computing an under-approximation of the qualitative winning region, i.e., states from which the parity condition can be enforced almost surely, and (II) computing the maximal probability of reaching this qualitative winning region.\r\nThe heart of our approach is a technique to symbolically compute the under-approximation of the qualitative winning region in step (I) via a finite-state abstraction of the original system as a \r\n-player parity game. Our abstraction procedure uses only the support of the probabilistic evolution; it does not use precise numerical transition probabilities. We prove that the winning set in the abstract -player game induces an under-approximation of the qualitative winning region in the original synthesis problem, along with a policy to solve it. By combining these contributions with (a) a symbolic fixpoint algorithm to solve \r\n-player games and (b) existing techniques for reachability policy synthesis in stochastic nonlinear systems, we get an abstraction-based algorithm for finding a lower bound on the maximal satisfaction probability.\r\nWe have implemented the abstraction-based algorithm in Mascot-SDS, where we combined the outlined abstraction step with our tool Genie (Majumdar et al., 2023) that solves \r\n-player parity games (through a reduction to Rabin games) more efficiently than existing algorithms. We evaluated our implementation on the nonlinear model of a perturbed bistable switch from the literature. We show empirically that the lower bound on the winning region computed by our approach is precise, by comparing against an over-approximation of the qualitative winning region. Moreover, our implementation outperforms a recently proposed tool for solving this problem by a large margin.","lang":"eng"}],"intvolume":" 51","month":"09","main_file_link":[{"url":"https://doi.org/10.1016/j.nahs.2023.101430","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["1751-570X"]},"ec_funded":1,"volume":51,"_id":"14400","status":"public","article_type":"original","type":"journal_article","date_updated":"2023-12-13T12:58:56Z","department":[{"_id":"ToHe"}]},{"citation":{"ista":"Zeng Z, Wodaczek F, Liu K, Stein F, Hutter J, Chen J, Cheng B. 2023. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 14, 6131.","chicago":"Zeng, Zezhu, Felix Wodaczek, Keyang Liu, Frederick Stein, Jürg Hutter, Ji Chen, and Bingqing Cheng. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41865-8.","ama":"Zeng Z, Wodaczek F, Liu K, et al. Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. 2023;14. doi:10.1038/s41467-023-41865-8","apa":"Zeng, Z., Wodaczek, F., Liu, K., Stein, F., Hutter, J., Chen, J., & Cheng, B. (2023). Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41865-8","short":"Z. Zeng, F. Wodaczek, K. Liu, F. Stein, J. Hutter, J. Chen, B. Cheng, Nature Communications 14 (2023).","ieee":"Z. Zeng et al., “Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Zeng, Zezhu, et al. “Mechanistic Insight on Water Dissociation on Pristine Low-Index TiO2 Surfaces from Machine Learning Molecular Dynamics Simulations.” Nature Communications, vol. 14, 6131, Springer Nature, 2023, doi:10.1038/s41467-023-41865-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2303.07433"],"isi":["001084354900008"],"pmid":["37783698"]},"article_processing_charge":"Yes","author":[{"full_name":"Zeng, Zezhu","last_name":"Zeng","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu"},{"id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","first_name":"Felix","orcid":"0009-0000-1457-795X","full_name":"Wodaczek, Felix","last_name":"Wodaczek"},{"first_name":"Keyang","last_name":"Liu","full_name":"Liu, Keyang"},{"full_name":"Stein, Frederick","last_name":"Stein","first_name":"Frederick"},{"first_name":"Jürg","full_name":"Hutter, Jürg","last_name":"Hutter"},{"first_name":"Ji","full_name":"Chen, Ji","last_name":"Chen"},{"full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"title":"Mechanistic insight on water dissociation on pristine low-index TiO2 surfaces from machine learning molecular dynamics simulations","article_number":"6131","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"year":"2023","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"02","date_created":"2023-10-15T22:01:10Z","doi":"10.1038/s41467-023-41865-8","date_published":"2023-10-02T00:00:00Z","acknowledgement":"F.S., J.H., and B.C. thank the Swiss National Supercomputing Centre (CSCS) for the generous allocation of CPU hours via production project s1108 at the Piz Daint supercomputer. B.C. acknowledges resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by EPSRC Tier-2 capital grant EP/P020259/1. J.C. acknowledges the Beijing Natural Science Foundation for support under grant No. JQ22001. F.S., and J.H. thank the Swiss Platform for Advanced Scientific Computing (PASC) via the 2021-2024 “Ab Initio Molecular Dynamics at the Exa-Scale” project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","date_updated":"2023-12-13T13:02:07Z","ddc":["540","000"],"department":[{"_id":"BiCh"},{"_id":"GradSch"}],"file_date_updated":"2023-10-16T07:34:49Z","_id":"14425","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14432","checksum":"7d1dffd36b672ec679f08f70ce79da87","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureComm_Zeng.pdf","date_created":"2023-10-16T07:34:49Z","creator":"dernst","file_size":3194116,"date_updated":"2023-10-16T07:34:49Z"}],"ec_funded":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/BingqingCheng/TiO2-water"}]},"volume":14,"abstract":[{"text":"Water adsorption and dissociation processes on pristine low-index TiO2 interfaces are important but poorly understood outside the well-studied anatase (101) and rutile (110). To understand these, we construct three sets of machine learning potentials that are simultaneously applicable to various TiO2 surfaces, based on three density-functional-theory approximations. Here we show the water dissociation free energies on seven pristine TiO2 surfaces, and predict that anatase (100), anatase (110), rutile (001), and rutile (011) favor water dissociation, anatase (101) and rutile (100) have mostly molecular adsorption, while the simulations of rutile (110) sensitively depend on the slab thickness and molecular adsorption is preferred with thick slabs. Moreover, using an automated algorithm, we reveal that these surfaces follow different types of atomistic mechanisms for proton transfer and water dissociation: one-step, two-step, or both. These mechanisms can be rationalized based on the arrangements of water molecules on the different surfaces. Our finding thus demonstrates that the different pristine TiO2 surfaces react with water in distinct ways, and cannot be represented using just the low-energy anatase (101) and rutile (110) surfaces.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","intvolume":" 14","month":"10"},{"acknowledgement":"The authors gratefully acknowledge funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). This work is also supported by a PhD fellowship funded by the Ecole Normale Supérieure de Paris-Saclay. Authors are also grateful to Benjamin Filider, who was of great help and support in the development of ideas. Eventually, we would like to thank Martin Singh, John M. Peters and an anonymous reviewer for their valuable comments and suggestions, which greatly improved the quality of the manuscript.","oa":1,"quality_controlled":"1","publisher":"Wiley","publication":"Journal of Advances in Modeling Earth Systems","day":"01","year":"2023","has_accepted_license":"1","isi":1,"date_created":"2023-10-29T23:01:15Z","date_published":"2023-10-01T00:00:00Z","doi":"10.1029/2022MS003477","article_number":"e2022MS003477","project":[{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical squall lines,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10. Wiley, 2023.","short":"S. Abramian, C.J. Muller, C. Risi, Journal of Advances in Modeling Earth Systems 15 (2023).","apa":"Abramian, S., Muller, C. J., & Risi, C. (2023). Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2022MS003477","ama":"Abramian S, Muller CJ, Risi C. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 2023;15(10). doi:10.1029/2022MS003477","mla":"Abramian, Sophie, et al. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 10, e2022MS003477, Wiley, 2023, doi:10.1029/2022MS003477.","ista":"Abramian S, Muller CJ, Risi C. 2023. Extreme precipitation in tropical squall lines. Journal of Advances in Modeling Earth Systems. 15(10), e2022MS003477.","chicago":"Abramian, Sophie, Caroline J Muller, and Camille Risi. “Extreme Precipitation in Tropical Squall Lines.” Journal of Advances in Modeling Earth Systems. Wiley, 2023. https://doi.org/10.1029/2022MS003477."},"title":"Extreme precipitation in tropical squall lines","article_processing_charge":"Yes","external_id":{"isi":["001084933600001"]},"author":[{"last_name":"Abramian","full_name":"Abramian, Sophie","first_name":"Sophie"},{"last_name":"Muller","full_name":"Muller, Caroline J","orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"first_name":"Camille","last_name":"Risi","full_name":"Risi, Camille"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Squall lines are substantially influenced by the interaction of low-level shear with cold pools associated with convective downdrafts. Beyond an optimal shear amplitude, squall lines tend to orient themselves at an angle with respect to the low-level shear. While the mechanisms behind squall line orientation seem to be increasingly well understood, uncertainties remain on the implications of this orientation. Roca and Fiolleau (2020, https://doi.org/10.1038/s43247-020-00015-4) show that long lived mesoscale convective systems, including squall lines, are disproportionately involved in rainfall extremes in the tropics. This article investigates the influence of the interaction between low-level shear and squall line outflow on squall line generated precipitation extrema in the tropics. Using a cloud resolving model, simulated squall lines in radiative convective equilibrium amid a shear-dominated regime (super optimal), a balanced regime (optimal), and an outflow dominated regime (suboptimal). Our results show that precipitation extremes in squall lines are 40% more intense in the case of optimal shear and remain 30% superior in the superoptimal regime relative to a disorganized case. With a theoretical scaling of precipitation extremes (C. Muller & Takayabu, 2020, https://doi.org/10.1088/1748-9326/ab7130), we show that the condensation rates control the amplification of precipitation extremes in tropical squall lines, mainly due to its change in vertical mass flux (dynamic component). The reduction of dilution by entrainment explains half of this change, consistent with Mulholland et al. (2021, https://doi.org/10.1175/jas-d-20-0299.1). The other half is explained by increased cloud-base velocity intensity in optimal and superoptimal squall lines."}],"intvolume":" 15","month":"10","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14470","checksum":"43e6a1a35b663843c7d3f8d0caaca1a5","file_size":1975210,"date_updated":"2023-10-30T13:31:42Z","creator":"dernst","file_name":"2023_JAMES_Abramian.pdf","date_created":"2023-10-30T13:31:42Z"}],"publication_status":"published","publication_identifier":{"eissn":["1942-2466"]},"ec_funded":1,"issue":"10","volume":15,"_id":"14453","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["550"],"date_updated":"2023-12-13T13:06:40Z","file_date_updated":"2023-10-30T13:31:42Z","department":[{"_id":"CaMu"}]},{"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"issn":["0935-9648","1521-4095"]},"month":"07","oa_version":"None","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"text":"High entropy alloys (HEAs) are highly suitable candidate catalysts for oxygen evolution and reduction reactions (OER/ORR) as they offer numerous parameters for optimizing the electronic structure and catalytic sites. Herein, FeCoNiMoW HEA nanoparticles are synthesized using a solution‐based low‐temperature approach. Such FeCoNiMoW nanoparticles show high entropy properties, subtle lattice distortions, and modulated electronic structure, leading to superior OER performance with an overpotential of 233 mV at 10 mA cm−2 and 276 mV at 100 mA cm−2. Density functional theory calculations reveal the electronic structures of the FeCoNiMoW active sites with an optimized d‐band center position that enables suitable adsorption of OOH* intermediates and reduces the Gibbs free energy barrier in the OER process. Aqueous zinc–air batteries (ZABs) based on this HEA demonstrate a high open circuit potential of 1.59 V, a peak power density of 116.9 mW cm−2, a specific capacity of 857 mAh gZn−1, and excellent stability for over 660 h of continuous charge–discharge cycles. Flexible and solid ZABs are also assembled and tested, displaying excellent charge–discharge performance at different bending angles. This work shows the significance of 4d/5d metal‐modulated electronic structure and optimized adsorption ability to improve the performance of OER/ORR, ZABs, and beyond.","lang":"eng"}],"department":[{"_id":"MaIb"}],"date_updated":"2023-12-13T13:03:23Z","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"status":"public","type":"journal_article","article_type":"original","_id":"14434","date_created":"2023-10-17T10:52:23Z","date_published":"2023-07-24T00:00:00Z","doi":"10.1002/adma.202303719","publication":"Advanced Materials","day":"24","year":"2023","isi":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"The authors acknowledge funding from Generalitat de Catalunya 2021 SGR 01581; the project COMBENERGY, PID2019-105490RB-C32, from the Spanish Ministerio de Ciencia e Innovación; the National Natural Science Foundation of China (22102002); the Anhui Provincial Natural Science Foundation (2108085QE192); Zhejiang Province key research and development project (2023C01191); the Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering (GrantNo.2022-K31); and The Key Research and Development Program of Hebei Province (20314305D). IREC is funded by the CERCA Programme from the Generalitat de Catalunya. L.L.Y. thanks the China Scholarship Council (CSC) for the scholarship support (202008130132). This research was supported by the Scientific Service Units (SSU) of ISTA (Institute of Science and Technology Austria) through resources provided by the Electron Microscopy Facility (EMF). S.L., S.H., and M.I. acknowledge funding by ISTA and the Werner Siemens.","title":"A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries","external_id":{"isi":["001083876900001"],"pmid":["37487245"]},"article_processing_charge":"No","author":[{"last_name":"He","full_name":"He, Ren","first_name":"Ren"},{"first_name":"Linlin","last_name":"Yang","full_name":"Yang, Linlin"},{"full_name":"Zhang, Yu","last_name":"Zhang","first_name":"Yu"},{"first_name":"Daochuan","last_name":"Jiang","full_name":"Jiang, Daochuan"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","first_name":"Seungho","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","last_name":"Lee"},{"last_name":"Horta","full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"first_name":"Zhifu","full_name":"Liang, Zhifu","last_name":"Liang"},{"last_name":"Lu","full_name":"Lu, Xuan","first_name":"Xuan"},{"full_name":"Ostovari Moghaddam, Ahmad","last_name":"Ostovari Moghaddam","first_name":"Ahmad"},{"last_name":"Li","full_name":"Li, Junshan","first_name":"Junshan"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ying","full_name":"Xu, Ying","last_name":"Xu"},{"first_name":"Yingtang","full_name":"Zhou, Yingtang","last_name":"Zhou"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"He, R., Yang, L., Zhang, Y., Jiang, D., Lee, S., Horta, S., … Cabot, A. (2023). A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202303719","ama":"He R, Yang L, Zhang Y, et al. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials. 2023. doi:10.1002/adma.202303719","ieee":"R. He et al., “A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries,” Advanced Materials. Wiley, 2023.","short":"R. He, L. Yang, Y. Zhang, D. Jiang, S. Lee, S. Horta, Z. Liang, X. Lu, A. Ostovari Moghaddam, J. Li, M. Ibáñez, Y. Xu, Y. Zhou, A. Cabot, Advanced Materials (2023).","mla":"He, Ren, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials, 2303719, Wiley, 2023, doi:10.1002/adma.202303719.","ista":"He R, Yang L, Zhang Y, Jiang D, Lee S, Horta S, Liang Z, Lu X, Ostovari Moghaddam A, Li J, Ibáñez M, Xu Y, Zhou Y, Cabot A. 2023. A 3d‐4d‐5d high entropy alloy as a bifunctional oxygen catalyst for robust aqueous zinc–air batteries. Advanced Materials., 2303719.","chicago":"He, Ren, Linlin Yang, Yu Zhang, Daochuan Jiang, Seungho Lee, Sharona Horta, Zhifu Liang, et al. “A 3d‐4d‐5d High Entropy Alloy as a Bifunctional Oxygen Catalyst for Robust Aqueous Zinc–Air Batteries.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202303719."},"project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"article_number":"2303719"},{"day":"09","language":[{"iso":"eng"}],"publication":"Advanced Materials","publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"isi":1,"publication_status":"accepted","year":"2023","date_published":"2023-08-09T00:00:00Z","doi":"10.1002/adma.202305128","date_created":"2023-10-17T10:53:56Z","oa_version":"None","pmid":1,"abstract":[{"text":"Low‐cost, safe, and environmental‐friendly rechargeable aqueous zinc‐ion batteries (ZIBs) are promising as next‐generation energy storage devices for wearable electronics among other applications. However, sluggish ionic transport kinetics and the unstable electrode structure during ionic insertion/extraction hampers their deployment. Herein, we propose a new cathode material based on a layered metal chalcogenide (LMC), bismuth telluride (Bi2Te3), coated with polypyrrole (PPy). Taking advantage of the PPy coating, the Bi2Te3@PPy composite presents strong ionic absorption affinity, high oxidation resistance, and high structural stability. The ZIBs based on Bi2Te3@PPy cathodes exhibit high capacities and ultra‐long lifespans of over 5000 cycles. They also present outstanding stability even under bending. In addition, we analyze here the reaction mechanism using in situ X‐ray diffraction, X‐ray photoelectron spectroscopy, and computational tools and demonstrate that, in the aqueous system, Zn2+ is not inserted into the cathode as previously assumed. In contrast, proton charge storage dominates the process. Overall, this work not only shows the great potential of LMCs as ZIBs cathode materials and the advantages of PPy coating, but also clarifies the charge/discharge mechanism in rechargeable ZIBs based on LMCs.","lang":"eng"}],"month":"08","quality_controlled":"1","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-13T13:03:53Z","citation":{"mla":"Zeng, Guifang, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials, 2305128, Wiley, doi:10.1002/adma.202305128.","short":"G. Zeng, Q. Sun, S. Horta, S. Wang, X. Lu, C. Zhang, J. Li, J. Li, L. Ci, Y. Tian, M. Ibáñez, A. Cabot, Advanced Materials (n.d.).","ieee":"G. Zeng et al., “A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries,” Advanced Materials. Wiley.","ama":"Zeng G, Sun Q, Horta S, et al. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. doi:10.1002/adma.202305128","apa":"Zeng, G., Sun, Q., Horta, S., Wang, S., Lu, X., Zhang, C., … Cabot, A. (n.d.). A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202305128","chicago":"Zeng, Guifang, Qing Sun, Sharona Horta, Shang Wang, Xuan Lu, Chaoyue Zhang, Jing Li, et al. “A Layered Bi2Te3@PPy Cathode for Aqueous Zinc Ion Batteries: Mechanism and Application in Printed Flexible Batteries.” Advanced Materials. Wiley, n.d. https://doi.org/10.1002/adma.202305128.","ista":"Zeng G, Sun Q, Horta S, Wang S, Lu X, Zhang C, Li J, Li J, Ci L, Tian Y, Ibáñez M, Cabot A. A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries. Advanced Materials., 2305128."},"title":"A layered Bi2Te3@PPy cathode for aqueous zinc ion batteries: Mechanism and application in printed flexible batteries","department":[{"_id":"MaIb"}],"author":[{"first_name":"Guifang","last_name":"Zeng","full_name":"Zeng, Guifang"},{"full_name":"Sun, Qing","last_name":"Sun","first_name":"Qing"},{"last_name":"Horta","full_name":"Horta, Sharona","first_name":"Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"last_name":"Wang","full_name":"Wang, Shang","first_name":"Shang"},{"last_name":"Lu","full_name":"Lu, Xuan","first_name":"Xuan"},{"first_name":"Chaoyue","full_name":"Zhang, Chaoyue","last_name":"Zhang"},{"first_name":"Jing","last_name":"Li","full_name":"Li, Jing"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Ci, Lijie","last_name":"Ci","first_name":"Lijie"},{"last_name":"Tian","full_name":"Tian, Yanhong","first_name":"Yanhong"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreu","full_name":"Cabot, Andreu","last_name":"Cabot"}],"external_id":{"isi":["001085681000001"],"pmid":["37555532"]},"article_processing_charge":"No","article_number":"2305128","_id":"14435","status":"public","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"article_type":"original","type":"journal_article"},{"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"month":"10","main_file_link":[{"url":"https://doi.org/10.1111/mec.17160","open_access":"1"}],"scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin.","lang":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2023-12-13T13:05:27Z","status":"public","type":"journal_article","article_type":"original","_id":"14463","date_created":"2023-10-29T23:01:17Z","doi":"10.1111/mec.17160","date_published":"2023-10-16T00:00:00Z","publication":"Molecular Ecology","day":"16","year":"2023","isi":1,"oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We would like to thank members of the Littorina team for their advice and feedback during this project. In particular, we thank Alan Le Moan, who inspired us to look at heterozygosity differences to identify inversions, and Katherine Hearn for helping with the PCA scripts. We thank Edinburgh Genomics for library preparation and sequencing. Sample collections, sequencing and data preparation were supported by the European Research Council (ERC-2015-AdG-693030- BARRIERS) and the Natural Environment Research Council (NE/P001610/1). The analysis was supported by the Swedish Research Council (vetenskaprådet; 2018-03695_VR) and the Portuguese Foundation for Science and Technology (Fundación para a Ciência e Tecnologia) through a research project (PTDC/BIA-EVL/1614/2021) and CEEC contract (2020.00275.CEECIND).","title":"Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana)","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37843465"],"isi":["001085119000001"]},"author":[{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"last_name":"Koch","full_name":"Koch, Eva L.","first_name":"Eva L."},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski","full_name":"Stankowski, Sean"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. 2023. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology.","chicago":"Reeve, James, Roger K. Butlin, Eva L. Koch, Sean Stankowski, and Rui Faria. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.17160.","short":"J. Reeve, R.K. Butlin, E.L. Koch, S. Stankowski, R. Faria, Molecular Ecology (2023).","ieee":"J. Reeve, R. K. Butlin, E. L. Koch, S. Stankowski, and R. Faria, “Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana),” Molecular Ecology. Wiley, 2023.","apa":"Reeve, J., Butlin, R. K., Koch, E. L., Stankowski, S., & Faria, R. (2023). Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. Wiley. https://doi.org/10.1111/mec.17160","ama":"Reeve J, Butlin RK, Koch EL, Stankowski S, Faria R. Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana). Molecular Ecology. 2023. doi:10.1111/mec.17160","mla":"Reeve, James, et al. “Chromosomal Inversion Polymorphisms Are Widespread across the Species Ranges of Rough Periwinkles (Littorina Saxatilis and L. Arcana).” Molecular Ecology, Wiley, 2023, doi:10.1111/mec.17160."}},{"article_number":"1287879","title":"Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment","external_id":{"isi":["001084841700001"],"pmid":["37854442"]},"article_processing_charge":"Yes","author":[{"full_name":"Narzisi, Antonio","last_name":"Narzisi","first_name":"Antonio"},{"full_name":"Halladay, Alycia","last_name":"Halladay","first_name":"Alycia"},{"first_name":"Gabriele","last_name":"Masi","full_name":"Masi, Gabriele"},{"last_name":"Novarino","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Catherine","last_name":"Lord","full_name":"Lord, Catherine"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 2023;14. doi:10.3389/fpsyt.2023.1287879","apa":"Narzisi, A., Halladay, A., Masi, G., Novarino, G., & Lord, C. (2023). Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. Frontiers. https://doi.org/10.3389/fpsyt.2023.1287879","short":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, C. Lord, Frontiers in Psychiatry 14 (2023).","ieee":"A. Narzisi, A. Halladay, G. Masi, G. Novarino, and C. Lord, “Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment,” Frontiers in Psychiatry, vol. 14. Frontiers, 2023.","mla":"Narzisi, Antonio, et al. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry, vol. 14, 1287879, Frontiers, 2023, doi:10.3389/fpsyt.2023.1287879.","ista":"Narzisi A, Halladay A, Masi G, Novarino G, Lord C. 2023. Tempering expectations: Considerations on the current state of stem cells therapy for autism treatment. Frontiers in Psychiatry. 14, 1287879.","chicago":"Narzisi, Antonio, Alycia Halladay, Gabriele Masi, Gaia Novarino, and Catherine Lord. “Tempering Expectations: Considerations on the Current State of Stem Cells Therapy for Autism Treatment.” Frontiers in Psychiatry. Frontiers, 2023. https://doi.org/10.3389/fpsyt.2023.1287879."},"oa":1,"publisher":"Frontiers","quality_controlled":"1","acknowledgement":"The author(s) declare that financial support was received for the research, authorship, and/or publication of this article. This work has been partially supported by Italian Ministry of Health Grant RC2023 (and the 5 × 1,000 voluntary contributions). The authors thank the children and their families with whom they work daily.","date_created":"2023-10-29T23:01:16Z","doi":"10.3389/fpsyt.2023.1287879","date_published":"2023-10-03T00:00:00Z","publication":"Frontiers in Psychiatry","day":"03","year":"2023","isi":1,"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"letter_note","type":"journal_article","_id":"14455","file_date_updated":"2023-10-30T12:48:40Z","department":[{"_id":"GaNo"}],"ddc":["570"],"date_updated":"2023-12-13T13:06:07Z","intvolume":" 14","month":"10","scopus_import":"1","pmid":1,"oa_version":"Published Version","volume":14,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_FrontiersPsychiatry_Narzisi.pdf","date_created":"2023-10-30T12:48:40Z","creator":"dernst","file_size":147878,"date_updated":"2023-10-30T12:48:40Z","success":1,"file_id":"14468","checksum":"0a76373e9a4c0fc199f80380de257e86","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1664-0640"]}},{"publication_identifier":{"eissn":["1432-0916"],"issn":["0010-3616"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"In the paper, we establish Squash Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich squash-type stadia whose convex arcs are homothetic. We also establish Stadium Rigidity Theorem—the dynamical spectral rigidity for piecewise analytic Bunimovich stadia whose flat boundaries are a priori fixed. In addition, for smooth Bunimovich squash-type stadia we compute the Lyapunov exponents along the maximal period two orbit, as well as the value of the Peierls’ Barrier function from the maximal marked length spectrum associated to the rotation number 2n/4n+1."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07330","open_access":"1"}],"month":"09","date_updated":"2023-12-13T13:02:44Z","department":[{"_id":"VaKa"}],"_id":"14427","article_type":"original","type":"journal_article","status":"public","isi":1,"year":"2023","day":"29","publication":"Communications in Mathematical Physics","date_published":"2023-09-29T00:00:00Z","doi":"10.1007/s00220-023-04837-z","date_created":"2023-10-15T22:01:11Z","acknowledgement":"VK acknowledges a partial support by the NSF grant DMS-1402164 and ERC Grant #885707. Discussions with Martin Leguil and Jacopo De Simoi were very useful. JC visited the University of Maryland and thanks for the hospitality. Also, JC was partially supported by the National Key Research and Development Program of China (No.2022YFA1005802), the NSFC Grant 12001392 and NSF of Jiangsu BK20200850. H.-K. Zhang is partially supported by the National Science Foundation (DMS-2220211), as well as Simons Foundation Collaboration Grants for Mathematicians (706383).","publisher":"Springer Nature","quality_controlled":"1","oa":1,"citation":{"mla":"Chen, Jianyu, et al. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics, Springer Nature, 2023, doi:10.1007/s00220-023-04837-z.","short":"J. Chen, V. Kaloshin, H.K. Zhang, Communications in Mathematical Physics (2023).","ieee":"J. Chen, V. Kaloshin, and H. K. Zhang, “Length spectrum rigidity for piecewise analytic Bunimovich billiards,” Communications in Mathematical Physics. Springer Nature, 2023.","apa":"Chen, J., Kaloshin, V., & Zhang, H. K. (2023). Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04837-z","ama":"Chen J, Kaloshin V, Zhang HK. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics. 2023. doi:10.1007/s00220-023-04837-z","chicago":"Chen, Jianyu, Vadim Kaloshin, and Hong Kun Zhang. “Length Spectrum Rigidity for Piecewise Analytic Bunimovich Billiards.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04837-z.","ista":"Chen J, Kaloshin V, Zhang HK. 2023. Length spectrum rigidity for piecewise analytic Bunimovich billiards. Communications in Mathematical Physics."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chen, Jianyu","last_name":"Chen","first_name":"Jianyu"},{"orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","first_name":"Vadim"},{"first_name":"Hong Kun","full_name":"Zhang, Hong Kun","last_name":"Zhang"}],"article_processing_charge":"No","external_id":{"arxiv":["1902.07330"],"isi":["001073177200001"]},"title":"Length spectrum rigidity for piecewise analytic Bunimovich billiards","project":[{"_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","name":"Spectral rigidity and integrability for billiards and geodesic flows","grant_number":"885707"}]},{"citation":{"ama":"Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 2023;34(7):737-760. doi:10.1142/S012905412342008X","apa":"Ambrus, Á., Csikós, M., Kiss, G., Pach, J., & Somlai, G. (2023). Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. World Scientific Publishing. https://doi.org/10.1142/S012905412342008X","short":"Á. Ambrus, M. Csikós, G. Kiss, J. Pach, G. Somlai, International Journal of Foundations of Computer Science 34 (2023) 737–760.","ieee":"Á. Ambrus, M. Csikós, G. Kiss, J. Pach, and G. Somlai, “Optimal embedded and enclosing isosceles triangles,” International Journal of Foundations of Computer Science, vol. 34, no. 7. World Scientific Publishing, pp. 737–760, 2023.","mla":"Ambrus, Áron, et al. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science, vol. 34, no. 7, World Scientific Publishing, 2023, pp. 737–60, doi:10.1142/S012905412342008X.","ista":"Ambrus Á, Csikós M, Kiss G, Pach J, Somlai G. 2023. Optimal embedded and enclosing isosceles triangles. International Journal of Foundations of Computer Science. 34(7), 737–760.","chicago":"Ambrus, Áron, Mónika Csikós, Gergely Kiss, János Pach, and Gábor Somlai. “Optimal Embedded and Enclosing Isosceles Triangles.” International Journal of Foundations of Computer Science. World Scientific Publishing, 2023. https://doi.org/10.1142/S012905412342008X."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2205.11637"],"isi":["001080874400001"]},"article_processing_charge":"No","author":[{"full_name":"Ambrus, Áron","last_name":"Ambrus","first_name":"Áron"},{"full_name":"Csikós, Mónika","last_name":"Csikós","first_name":"Mónika"},{"first_name":"Gergely","full_name":"Kiss, Gergely","last_name":"Kiss"},{"id":"E62E3130-B088-11EA-B919-BF823C25FEA4","first_name":"János","last_name":"Pach","full_name":"Pach, János"},{"first_name":"Gábor","full_name":"Somlai, Gábor","last_name":"Somlai"}],"title":"Optimal embedded and enclosing isosceles triangles","year":"2023","isi":1,"publication":"International Journal of Foundations of Computer Science","day":"05","page":"737-760","date_created":"2023-10-29T23:01:18Z","date_published":"2023-10-05T00:00:00Z","doi":"10.1142/S012905412342008X","oa":1,"publisher":"World Scientific Publishing","quality_controlled":"1","date_updated":"2023-12-13T13:04:55Z","department":[{"_id":"HeEd"}],"_id":"14464","article_type":"original","type":"journal_article","status":"public","publication_status":"published","publication_identifier":{"eissn":["1793-6373"],"issn":["0129-0541"]},"language":[{"iso":"eng"}],"issue":"7","volume":34,"abstract":[{"text":"Given a triangle Δ, we study the problem of determining the smallest enclosing and largest embedded isosceles triangles of Δ with respect to area and perimeter. This problem was initially posed by Nandakumar [17, 22] and was first studied by Kiss, Pach, and Somlai [13], who showed that if Δ′ is the smallest area isosceles triangle containing Δ, then Δ′ and Δ share a side and an angle. In the present paper, we prove that for any triangle Δ, every maximum area isosceles triangle embedded in Δ and every maximum perimeter isosceles triangle embedded in Δ shares a side and an angle with Δ. Somewhat surprisingly, the case of minimum perimeter enclosing triangles is different: there are infinite families of triangles Δ whose minimum perimeter isosceles containers do not share a side and an angle with Δ.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.11637"}],"scopus_import":"1","intvolume":" 34","month":"10"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14449","file_date_updated":"2023-10-30T13:38:48Z","department":[{"_id":"ScienComp"}],"date_updated":"2023-12-13T13:07:21Z","ddc":["000"],"scopus_import":"1","intvolume":" 14","month":"09","abstract":[{"lang":"eng","text":"The rapid development of machine learning (ML) techniques has opened up the data-dense field of microbiome research for novel therapeutic, diagnostic, and prognostic applications targeting a wide range of disorders, which could substantially improve healthcare practices in the era of precision medicine. However, several challenges must be addressed to exploit the benefits of ML in this field fully. In particular, there is a need to establish “gold standard” protocols for conducting ML analysis experiments and improve interactions between microbiome researchers and ML experts. The Machine Learning Techniques in Human Microbiome Studies (ML4Microbiome) COST Action CA18131 is a European network established in 2019 to promote collaboration between discovery-oriented microbiome researchers and data-driven ML experts to optimize and standardize ML approaches for microbiome analysis. This perspective paper presents the key achievements of ML4Microbiome, which include identifying predictive and discriminatory ‘omics’ features, improving repeatability and comparability, developing automation procedures, and defining priority areas for the novel development of ML methods targeting the microbiome. The insights gained from ML4Microbiome will help to maximize the potential of ML in microbiome research and pave the way for new and improved healthcare practices."}],"pmid":1,"oa_version":"Published Version","volume":14,"publication_status":"published","publication_identifier":{"eissn":["1664-302X"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":505078,"date_updated":"2023-10-30T13:38:48Z","file_name":"2023_FrontiersMicrobiology_DElia.pdf","date_created":"2023-10-30T13:38:48Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"14471","checksum":"6c0acdd8fa111a699826957b8dff19d5"}],"article_number":"1257002","article_processing_charge":"Yes","external_id":{"pmid":["37808321"],"isi":["001080536000001"]},"author":[{"full_name":"D’Elia, Domenica","last_name":"D’Elia","first_name":"Domenica"},{"last_name":"Truu","full_name":"Truu, Jaak","first_name":"Jaak"},{"full_name":"Lahti, Leo","last_name":"Lahti","first_name":"Leo"},{"first_name":"Magali","last_name":"Berland","full_name":"Berland, Magali"},{"last_name":"Papoutsoglou","full_name":"Papoutsoglou, Georgios","first_name":"Georgios"},{"last_name":"Ceci","full_name":"Ceci, Michelangelo","first_name":"Michelangelo"},{"first_name":"Aldert","last_name":"Zomer","full_name":"Zomer, Aldert"},{"last_name":"Lopes","full_name":"Lopes, Marta B.","first_name":"Marta B."},{"full_name":"Ibrahimi, Eliana","last_name":"Ibrahimi","first_name":"Eliana"},{"last_name":"Gruca","full_name":"Gruca, Aleksandra","first_name":"Aleksandra"},{"last_name":"Nechyporenko","full_name":"Nechyporenko, Alina","first_name":"Alina"},{"full_name":"Frohme, Marcus","last_name":"Frohme","first_name":"Marcus"},{"full_name":"Klammsteiner, Thomas","last_name":"Klammsteiner","first_name":"Thomas"},{"first_name":"Enrique Carrillo De Santa","last_name":"Pau","full_name":"Pau, Enrique Carrillo De Santa"},{"first_name":"Laura Judith","last_name":"Marcos-Zambrano","full_name":"Marcos-Zambrano, Laura Judith"},{"first_name":"Karel","last_name":"Hron","full_name":"Hron, Karel"},{"full_name":"Pio, Gianvito","last_name":"Pio","first_name":"Gianvito"},{"first_name":"Andrea","full_name":"Simeon, Andrea","last_name":"Simeon"},{"last_name":"Suharoschi","full_name":"Suharoschi, Ramona","first_name":"Ramona"},{"first_name":"Isabel","last_name":"Moreno-Indias","full_name":"Moreno-Indias, Isabel"},{"first_name":"Andriy","last_name":"Temko","full_name":"Temko, Andriy"},{"first_name":"Miroslava","full_name":"Nedyalkova, Miroslava","last_name":"Nedyalkova"},{"full_name":"Apostol, Elena Simona","last_name":"Apostol","first_name":"Elena Simona"},{"last_name":"Truică","full_name":"Truică, Ciprian Octavian","first_name":"Ciprian Octavian"},{"first_name":"Rajesh","full_name":"Shigdel, Rajesh","last_name":"Shigdel"},{"first_name":"Jasminka Hasić","last_name":"Telalović","full_name":"Telalović, Jasminka Hasić"},{"first_name":"Erik","full_name":"Bongcam-Rudloff, Erik","last_name":"Bongcam-Rudloff"},{"last_name":"Przymus","full_name":"Przymus, Piotr","first_name":"Piotr"},{"full_name":"Jordamović, Naida Babić","last_name":"Jordamović","first_name":"Naida Babić"},{"last_name":"Falquet","full_name":"Falquet, Laurent","first_name":"Laurent"},{"first_name":"Sonia","full_name":"Tarazona, Sonia","last_name":"Tarazona"},{"first_name":"Alexia","last_name":"Sampri","full_name":"Sampri, Alexia"},{"first_name":"Gaetano","last_name":"Isola","full_name":"Isola, Gaetano"},{"full_name":"Pérez-Serrano, David","last_name":"Pérez-Serrano","first_name":"David"},{"full_name":"Trajkovik, Vladimir","last_name":"Trajkovik","first_name":"Vladimir"},{"last_name":"Klucar","full_name":"Klucar, Lubos","first_name":"Lubos"},{"last_name":"Loncar-Turukalo","full_name":"Loncar-Turukalo, Tatjana","first_name":"Tatjana"},{"last_name":"Havulinna","full_name":"Havulinna, Aki S.","first_name":"Aki S."},{"last_name":"Jansen","full_name":"Jansen, Christian","first_name":"Christian","id":"837b2259-bcc9-11ed-a196-ae55927bc6e2"},{"last_name":"Bertelsen","full_name":"Bertelsen, Randi J.","first_name":"Randi J."},{"last_name":"Claesson","full_name":"Claesson, Marcus Joakim","first_name":"Marcus Joakim"}],"title":"Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action","citation":{"ieee":"D. D’Elia et al., “Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action,” Frontiers in Microbiology, vol. 14. Frontiers, 2023.","short":"D. D’Elia, J. Truu, L. Lahti, M. Berland, G. Papoutsoglou, M. Ceci, A. Zomer, M.B. Lopes, E. Ibrahimi, A. Gruca, A. Nechyporenko, M. Frohme, T. Klammsteiner, E.C.D.S. Pau, L.J. Marcos-Zambrano, K. Hron, G. Pio, A. Simeon, R. Suharoschi, I. Moreno-Indias, A. Temko, M. Nedyalkova, E.S. Apostol, C.O. Truică, R. Shigdel, J.H. Telalović, E. Bongcam-Rudloff, P. Przymus, N.B. Jordamović, L. Falquet, S. Tarazona, A. Sampri, G. Isola, D. Pérez-Serrano, V. Trajkovik, L. Klucar, T. Loncar-Turukalo, A.S. Havulinna, C. Jansen, R.J. Bertelsen, M.J. Claesson, Frontiers in Microbiology 14 (2023).","apa":"D’Elia, D., Truu, J., Lahti, L., Berland, M., Papoutsoglou, G., Ceci, M., … Claesson, M. J. (2023). Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2023.1257002","ama":"D’Elia D, Truu J, Lahti L, et al. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 2023;14. doi:10.3389/fmicb.2023.1257002","mla":"D’Elia, Domenica, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology, vol. 14, 1257002, Frontiers, 2023, doi:10.3389/fmicb.2023.1257002.","ista":"D’Elia D, Truu J, Lahti L, Berland M, Papoutsoglou G, Ceci M, Zomer A, Lopes MB, Ibrahimi E, Gruca A, Nechyporenko A, Frohme M, Klammsteiner T, Pau ECDS, Marcos-Zambrano LJ, Hron K, Pio G, Simeon A, Suharoschi R, Moreno-Indias I, Temko A, Nedyalkova M, Apostol ES, Truică CO, Shigdel R, Telalović JH, Bongcam-Rudloff E, Przymus P, Jordamović NB, Falquet L, Tarazona S, Sampri A, Isola G, Pérez-Serrano D, Trajkovik V, Klucar L, Loncar-Turukalo T, Havulinna AS, Jansen C, Bertelsen RJ, Claesson MJ. 2023. Advancing microbiome research with machine learning: Key findings from the ML4Microbiome COST action. Frontiers in Microbiology. 14, 1257002.","chicago":"D’Elia, Domenica, Jaak Truu, Leo Lahti, Magali Berland, Georgios Papoutsoglou, Michelangelo Ceci, Aldert Zomer, et al. “Advancing Microbiome Research with Machine Learning: Key Findings from the ML4Microbiome COST Action.” Frontiers in Microbiology. Frontiers, 2023. https://doi.org/10.3389/fmicb.2023.1257002."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Frontiers","acknowledgement":"This study is based upon work from COST Action ML4Microbiome “Statistical and machine learning techniques in human microbiome studies” (CA18131), supported by COST (European Cooperation in Science and Technology), www.cost.eu. MB acknowledges support through the Metagenopolis grant ANR-11-DPBS-0001. IM-I acknowledges support by the “Miguel Servet Type II” program (CPII21/00013) of the ISCIII-Madrid (Spain), co-financed by the FEDER.\r\nThe authors are grateful to all COST Action CA18131 “Statistical and machine learning techniques in human microbiome studies” members for their contribution to the COST Action objectives, and to COST (European Cooperation in Science and Technology) for the economic support, www.cost.eu. WG2 and WG3 thank Emmanuelle Le Chatelier and Pauline Barbet (Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France) for preparing the shotgun CRC benchmark dataset.","date_created":"2023-10-22T22:01:16Z","date_published":"2023-09-25T00:00:00Z","doi":"10.3389/fmicb.2023.1257002","year":"2023","isi":1,"has_accepted_license":"1","publication":"Frontiers in Microbiology","day":"25"},{"intvolume":" 107","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a variational quantum algorithm, where a quantum computer implements a variational ansatz consisting of p layers of alternating unitary operators and a classical computer is used to optimize the variational parameters. For a random initialization, the optimization typically leads to local minima with poor performance, motivating the search for initialization strategies of QAOA variational parameters. Although numerous heuristic initializations exist, an analytical understanding and performance guarantees for large p remain evasive.We introduce a greedy initialization of QAOA which guarantees improving performance with an increasing number of layers. Our main result is an analytic construction of 2p + 1 transition states—saddle points with a unique negative curvature direction—for QAOA with p + 1 layers that use the local minimum of QAOA with p layers. Transition states connect to new local minima, which are guaranteed to lower the energy compared to the minimum found for p layers. We use the GREEDY procedure to navigate the exponentially increasing with p number of local minima resulting from the recursive application of our analytic construction. The performance of the GREEDY procedure matches available initialization strategies while providing a guarantee for the minimal energy to decrease with an increasing number of layers p. ","lang":"eng"}],"ec_funded":1,"related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"volume":107,"issue":"6","language":[{"iso":"eng"}],"file":[{"checksum":"0d71423888eeccaa60d8f41197f26306","file_id":"13131","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-06-13T07:28:36Z","file_name":"2023_PhysRevA_Sack.pdf","date_updated":"2023-06-13T07:28:36Z","file_size":2524611,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"13125","department":[{"_id":"MaSe"}],"file_date_updated":"2023-06-13T07:28:36Z","ddc":["530"],"date_updated":"2023-12-13T14:47:25Z","oa":1,"quality_controlled":"1","publisher":"American Physical Society","acknowledgement":"We thank V. Verteletskyi for a joint collaboration on numerical studies of the QAOA during his internship at ISTA that inspired analytic results on TS reported in this work. We acknowledge A. A. Mele and M. Brooks for discussions and D. Egger, P. Love, and D. Wierichs for valuable feedback on the manuscript. S.H.S., R.A.M., and M.S. acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899). R.K. is supported by the SFB BeyondC (Grant No. F7107-N38) and the project QuantumReady (FFG 896217). ","date_created":"2023-06-07T06:57:32Z","doi":"10.1103/physreva.107.062404","date_published":"2023-06-02T00:00:00Z","publication":"Physical Review A","day":"02","year":"2023","isi":1,"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"article_number":"062404","title":"Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement","article_processing_charge":"No","external_id":{"arxiv":["2209.01159"],"isi":["001016927100012"]},"author":[{"first_name":"Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","full_name":"Sack, Stefan","orcid":"0000-0001-5400-8508"},{"orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos","first_name":"Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425"},{"first_name":"Richard","last_name":"Kueng","full_name":"Kueng, Richard"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. 2023. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 107(6), 062404.","chicago":"Sack, Stefan, Raimel A Medina Ramos, Richard Kueng, and Maksym Serbyn. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A. American Physical Society, 2023. https://doi.org/10.1103/physreva.107.062404.","ama":"Sack S, Medina Ramos RA, Kueng R, Serbyn M. Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. 2023;107(6). doi:10.1103/physreva.107.062404","apa":"Sack, S., Medina Ramos, R. A., Kueng, R., & Serbyn, M. (2023). Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement. Physical Review A. American Physical Society. https://doi.org/10.1103/physreva.107.062404","ieee":"S. Sack, R. A. Medina Ramos, R. Kueng, and M. Serbyn, “Recursive greedy initialization of the quantum approximate optimization algorithm with guaranteed improvement,” Physical Review A, vol. 107, no. 6. American Physical Society, 2023.","short":"S. Sack, R.A. Medina Ramos, R. Kueng, M. Serbyn, Physical Review A 107 (2023).","mla":"Sack, Stefan, et al. “Recursive Greedy Initialization of the Quantum Approximate Optimization Algorithm with Guaranteed Improvement.” Physical Review A, vol. 107, no. 6, 062404, American Physical Society, 2023, doi:10.1103/physreva.107.062404."}},{"oa":1,"publisher":"Springer Nature","quality_controlled":"1","date_created":"2023-10-22T22:01:14Z","doi":"10.1007/s11856-023-2521-9","date_published":"2023-09-01T00:00:00Z","page":"675-717","publication":"Israel Journal of Mathematics","day":"01","year":"2023","isi":1,"has_accepted_license":"1","title":"Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001081646400010"]},"author":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"last_name":"Wild","full_name":"Wild, Pascal","id":"4C20D868-F248-11E8-B48F-1D18A9856A87","first_name":"Pascal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics. Springer Nature, 2023. https://doi.org/10.1007/s11856-023-2521-9.","ista":"Wagner U, Wild P. 2023. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 256(2), 675–717.","mla":"Wagner, Uli, and Pascal Wild. “Coboundary Expansion, Equivariant Overlap, and Crossing Numbers of Simplicial Complexes.” Israel Journal of Mathematics, vol. 256, no. 2, Springer Nature, 2023, pp. 675–717, doi:10.1007/s11856-023-2521-9.","apa":"Wagner, U., & Wild, P. (2023). Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-023-2521-9","ama":"Wagner U, Wild P. Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes. Israel Journal of Mathematics. 2023;256(2):675-717. doi:10.1007/s11856-023-2521-9","short":"U. Wagner, P. Wild, Israel Journal of Mathematics 256 (2023) 675–717.","ieee":"U. Wagner and P. Wild, “Coboundary expansion, equivariant overlap, and crossing numbers of simplicial complexes,” Israel Journal of Mathematics, vol. 256, no. 2. Springer Nature, pp. 675–717, 2023."},"intvolume":" 256","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We prove the following quantitative Borsuk–Ulam-type result (an equivariant analogue of Gromov’s Topological Overlap Theorem): Let X be a free ℤ/2-complex of dimension d with coboundary expansion at least ηk in dimension 0 ≤ k < d. Then for every equivariant map F: X →ℤ/2 ℝd, the fraction of d-simplices σ of X with 0 ∈ F (σ) is at least 2−d Π d−1k=0ηk.\r\n\r\nAs an application, we show that for every sufficiently thick d-dimensional spherical building Y and every map f: Y → ℝ2d, we have f(σ) ∩ f(τ) ≠ ∅ for a constant fraction μd > 0 of pairs {σ, τ} of d-simplices of Y. In particular, such complexes are non-embeddable into ℝ2d, which proves a conjecture of Tancer and Vorwerk for sufficiently thick spherical buildings.\r\n\r\nWe complement these results by upper bounds on the coboundary expansion of two families of simplicial complexes; this indicates some limitations to the bounds one can obtain by straighforward applications of the quantitative Borsuk–Ulam theorem. Specifically, we prove\r\n\r\n• an upper bound of (d + 1)/2d on the normalized (d − 1)-th coboundary expansion constant of complete (d + 1)-partite d-dimensional complexes (under a mild divisibility assumption on the sizes of the parts); and\r\n\r\n• an upper bound of (d + 1)/2d + ε on the normalized (d − 1)-th coboundary expansion of the d-dimensional spherical building associated with GLd+2(Fq) for any ε > 0 and sufficiently large q. This disproves, in a rather strong sense, a conjecture of Lubotzky, Meshulam and Mozes.","lang":"eng"}],"issue":"2","volume":256,"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14475","checksum":"fbb05619fe4b650f341cc730425dd9c3","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_IsraelJourMath_Wagner.pdf","date_created":"2023-10-31T11:20:31Z","file_size":623787,"date_updated":"2023-10-31T11:20:31Z","creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1565-8511"],"issn":["0021-2172"]},"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14445","file_date_updated":"2023-10-31T11:20:31Z","department":[{"_id":"UlWa"}],"ddc":["510"],"date_updated":"2023-12-13T13:09:07Z"},{"title":"New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana","author":[{"first_name":"Kristýna","full_name":"Bieleszová, Kristýna","last_name":"Bieleszová"},{"first_name":"Pavel","full_name":"Hladík, Pavel","last_name":"Hladík"},{"last_name":"Kubala","full_name":"Kubala, Martin","first_name":"Martin"},{"first_name":"Richard","last_name":"Napier","full_name":"Napier, Richard"},{"last_name":"Brunoni","full_name":"Brunoni, Federica","first_name":"Federica"},{"full_name":"Gelová, Zuzana","orcid":"0000-0003-4783-1752","last_name":"Gelová","first_name":"Zuzana","id":"0AE74790-0E0B-11E9-ABC7-1ACFE5697425"},{"id":"7c417475-8972-11ed-ae7b-8b674ca26986","first_name":"Lukas","last_name":"Fiedler","full_name":"Fiedler, Lukas"},{"id":"57a1567c-8314-11eb-9063-c9ddc3451a54","first_name":"Ivan","full_name":"Kulich, Ivan","last_name":"Kulich"},{"last_name":"Strnad","full_name":"Strnad, Miroslav","first_name":"Miroslav"},{"first_name":"Karel","last_name":"Doležal","full_name":"Doležal, Karel"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Žukauskaitė, Asta","last_name":"Žukauskaitė","first_name":"Asta"}],"external_id":{"isi":["001084334300001"]},"article_processing_charge":"Yes (via OA deal)","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Bieleszová K, Hladík P, Kubala M, Napier R, Brunoni F, Gelová Z, Fiedler L, Kulich I, Strnad M, Doležal K, Novák O, Friml J, Žukauskaitė A. 2023. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation.","chicago":"Bieleszová, Kristýna, Pavel Hladík, Martin Kubala, Richard Napier, Federica Brunoni, Zuzana Gelová, Lukas Fiedler, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation. Springer Nature, 2023. https://doi.org/10.1007/s10725-023-01083-0.","ama":"Bieleszová K, Hladík P, Kubala M, et al. New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. 2023. doi:10.1007/s10725-023-01083-0","apa":"Bieleszová, K., Hladík, P., Kubala, M., Napier, R., Brunoni, F., Gelová, Z., … Žukauskaitė, A. (2023). New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana. Plant Growth Regulation. Springer Nature. https://doi.org/10.1007/s10725-023-01083-0","ieee":"K. Bieleszová et al., “New fluorescent auxin derivatives: anti-auxin activity and accumulation patterns in Arabidopsis thaliana,” Plant Growth Regulation. Springer Nature, 2023.","short":"K. Bieleszová, P. Hladík, M. Kubala, R. Napier, F. Brunoni, Z. Gelová, L. Fiedler, I. Kulich, M. Strnad, K. Doležal, O. Novák, J. Friml, A. Žukauskaitė, Plant Growth Regulation (2023).","mla":"Bieleszová, Kristýna, et al. “New Fluorescent Auxin Derivatives: Anti-Auxin Activity and Accumulation Patterns in Arabidopsis Thaliana.” Plant Growth Regulation, Springer Nature, 2023, doi:10.1007/s10725-023-01083-0."},"doi":"10.1007/s10725-023-01083-0","date_published":"2023-10-13T00:00:00Z","date_created":"2023-10-22T22:01:15Z","day":"13","publication":"Plant Growth Regulation","isi":1,"year":"2023","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"The authors would like to thank Karolína Kubiasová and Iñigo Saiz-Fernández for valuable scientific discussions. Open access publishing supported by the National Technical Library in Prague. This work was supported by the Palacký University Olomouc Young Researcher Grant Competition (JG_2020_002), by the Internal Grant Agency of Palacký University Olomouc (IGA_PrF_2023_016, IGA_PrF_2023_031), by the Ministry of Education, Youth and Sports of the Czech Republic through the European Regional Development Fund-Project Plants as a tool for sustainable global development (CZ.02.1.01/0.0/0.0/16_019/0000827) and the project Support of mobility at Palacký University Olomouc II. (CZ.02.2.69/0.0/0.0/18_053/0016919). The Biacore T200 SPR instrument was provided by the WISB Research Technology Facility within the School of Life Sciences, University of Warwick.","department":[{"_id":"JiFr"}],"date_updated":"2023-12-13T13:08:25Z","status":"public","type":"journal_article","article_type":"original","_id":"14447","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1573-5087"],"issn":["0167-6903"]},"publication_status":"epub_ahead","month":"10","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10725-023-01083-0","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Auxin belongs among major phytohormones and governs multiple aspects of plant growth and development. The establishment of auxin concentration gradients, determines, among other processes, plant organ positioning and growth responses to environmental stimuli.\r\nHerein we report the synthesis of new NBD- or DNS-labelled IAA derivatives and the elucidation of their biological activity, fluorescence properties and subcellular accumulation patterns in planta. These novel compounds did not show auxin-like activity, but instead antagonized physiological auxin effects. The DNS-labelled derivatives FL5 and FL6 showed strong anti-auxin activity in roots and hypocotyls, which also occurred at the level of gene transcription as confirmed by quantitative PCR analysis. The auxin antagonism of our derivatives was further demonstrated in vitro using an SPR-based binding assay. The NBD-labelled compound FL4 with the best fluorescence properties proved to be unsuitable to study auxin accumulation patterns in planta. On the other hand, the strongest anti-auxin activity possessing compounds FL5 and FL6 could be useful to study binding mechanisms to auxin receptors and for manipulations of auxin-regulated processes."}]},{"article_processing_charge":"No","author":[{"last_name":"Sack","orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","first_name":"Stefan"}],"title":"Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems","citation":{"chicago":"Sack, Stefan. “Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14622.","ista":"Sack S. 2023. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria.","mla":"Sack, Stefan. Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14622.","short":"S. Sack, Improving Variational Quantum Algorithms: Innovative Initialization Techniques and Extensions to Qudit Systems, Institute of Science and Technology Austria, 2023.","ieee":"S. Sack, “Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems,” Institute of Science and Technology Austria, 2023.","apa":"Sack, S. (2023). Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14622","ama":"Sack S. Improving variational quantum algorithms: Innovative initialization techniques and extensions to qudit systems. 2023. doi:10.15479/at:ista:14622"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","project":[{"_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d","name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices"},{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"850899","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"page":"142","date_created":"2023-11-28T10:58:13Z","doi":"10.15479/at:ista:14622","date_published":"2023-11-30T00:00:00Z","year":"2023","has_accepted_license":"1","day":"30","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"file_date_updated":"2023-12-01T11:10:46Z","date_updated":"2023-12-13T14:47:25Z","supervisor":[{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"}],"ddc":["530"],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"type":"dissertation","status":"public","_id":"14622","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"related_material":{"record":[{"id":"11471","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"13125","status":"public"},{"relation":"part_of_dissertation","id":"9760","status":"public"}]},"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-11-30","file_id":"14635","checksum":"068fd3570506ec42b2faa390de784bc4","file_size":11947523,"date_updated":"2023-12-01T11:10:46Z","creator":"ssack","file_name":"PhD_Thesis.pdf","date_created":"2023-11-30T15:53:10Z"},{"creator":"ssack","file_size":18422964,"date_updated":"2023-12-01T11:10:46Z","file_name":"PhD Thesis (1).zip","date_created":"2023-11-30T15:54:11Z","relation":"source_file","access_level":"closed","content_type":"application/zip","file_id":"14636","checksum":"0fa3bc0d108aed0ac59d2c6beef2220a"}],"alternative_title":["ISTA Thesis"],"month":"11","oa_version":"Published Version"},{"_id":"14683","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"review","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Neuroscience"],"status":"public","date_updated":"2023-12-18T08:06:14Z","ddc":["570"],"department":[{"_id":"SiHi"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice and high-resolution phenotyping at the individual cell level. Here, we present a protocol for isolating MADM-labeled cells with high yield for downstream molecular analyses using fluorescence-activated cell sorting (FACS). We describe steps for generating MADM-labeled mice, perfusion, single-cell suspension, and debris removal. We then detail procedures for cell sorting by FACS and downstream analysis. This protocol is suitable for embryonic to adult mice.\r\nFor complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).1"}],"oa_version":"Submitted Version","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.xpro.2023.102771","open_access":"1"}],"scopus_import":"1","intvolume":" 5","month":"12","publication_status":"epub_ahead","publication_identifier":{"issn":["2666-1667"]},"language":[{"iso":"eng"}],"ec_funded":1,"volume":5,"issue":"1","article_number":"102771","project":[{"grant_number":"T0101031","name":"Role of Eed in neural stem cell lineage progression","call_identifier":"FWF","_id":"268F8446-B435-11E9-9278-68D0E5697425"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"F07805","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"citation":{"ama":"Amberg N, Cheung GT, Hippenmeyer S. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 2023;5(1). doi:10.1016/j.xpro.2023.102771","apa":"Amberg, N., Cheung, G. T., & Hippenmeyer, S. (2023). Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2023.102771","short":"N. Amberg, G.T. Cheung, S. Hippenmeyer, STAR Protocols 5 (2023).","ieee":"N. Amberg, G. T. Cheung, and S. Hippenmeyer, “Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry,” STAR Protocols, vol. 5, no. 1. Elsevier, 2023.","mla":"Amberg, Nicole, et al. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols, vol. 5, no. 1, 102771, Elsevier, 2023, doi:10.1016/j.xpro.2023.102771.","ista":"Amberg N, Cheung GT, Hippenmeyer S. 2023. Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry. STAR Protocols. 5(1), 102771.","chicago":"Amberg, Nicole, Giselle T Cheung, and Simon Hippenmeyer. “Protocol for Sorting Cells from Mouse Brains Labeled with Mosaic Analysis with Double Markers by Flow Cytometry.” STAR Protocols. Elsevier, 2023. https://doi.org/10.1016/j.xpro.2023.102771."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["38070137"]},"article_processing_charge":"No","author":[{"full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"}],"title":"Protocol for sorting cells from mouse brains labeled with mosaic analysis with double markers by flow cytometry","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Imaging & Optics Facility (IOF) and Preclinical Facilities (PCF). N.A. received support from FWF Firnberg-Programme (T 1031). G.C. received support from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411 as an ISTplus postdoctoral fellow. This work was also supported by IST Austria institutional funds, FWF SFB F78 to S.H., and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","oa":1,"quality_controlled":"1","publisher":"Elsevier","year":"2023","publication":"STAR Protocols","day":"08","date_created":"2023-12-13T11:48:05Z","date_published":"2023-12-08T00:00:00Z","doi":"10.1016/j.xpro.2023.102771"},{"date_published":"2023-11-28T00:00:00Z","doi":"10.1007/s40072-023-00319-4","date_created":"2023-02-02T10:45:47Z","has_accepted_license":"1","year":"2023","day":"28","publication":"Stochastics and Partial Differential Equations: Analysis and Computations","publisher":"Springer Nature","oa":1,"acknowledgement":"The author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).\r\nThe author thanks Lorenzo Dello Schiavo, Lucio Galeati and Mark Veraar for helpful comments. The author acknowledges Caterina Balzotti for her support in creating the picture. The author\r\nthanks the anonymous referee for helpful comments. ","author":[{"id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","first_name":"Antonio","last_name":"Agresti","orcid":"0000-0002-9573-2962","full_name":"Agresti, Antonio"}],"external_id":{"arxiv":["2207.08293"]},"article_processing_charge":"No","title":"Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations","citation":{"mla":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations, Springer Nature, 2023, doi:10.1007/s40072-023-00319-4.","short":"A. Agresti, Stochastics and Partial Differential Equations: Analysis and Computations (2023).","ieee":"A. Agresti, “Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations,” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023.","ama":"Agresti A. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. 2023. doi:10.1007/s40072-023-00319-4","apa":"Agresti, A. (2023). Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature. https://doi.org/10.1007/s40072-023-00319-4","chicago":"Agresti, Antonio. “Delayed Blow-up and Enhanced Diffusion by Transport Noise for Systems of Reaction-Diffusion Equations.” Stochastics and Partial Differential Equations: Analysis and Computations. Springer Nature, 2023. https://doi.org/10.1007/s40072-023-00319-4.","ista":"Agresti A. 2023. Delayed blow-up and enhanced diffusion by transport noise for systems of reaction-diffusion equations. Stochastics and Partial Differential Equations: Analysis and Computations."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"948819","name":"Bridging Scales in Random Materials","call_identifier":"H2020","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"ec_funded":1,"publication_identifier":{"eissn":["2194-041X"],"issn":["2194-0401"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s40072-023-00319-4"}],"month":"11","abstract":[{"text":"This paper is concerned with the problem of regularization by noise of systems of reaction–diffusion equations with mass control. It is known that strong solutions to such systems of PDEs may blow-up in finite time. Moreover, for many systems of practical interest, establishing whether the blow-up occurs or not is an open question. Here we prove that a suitable multiplicative noise of transport type has a regularizing effect. More precisely, for both a sufficiently noise intensity and a high spectrum, the blow-up of strong solutions is delayed up to an arbitrary large time. Global existence is shown for the case of exponentially decreasing mass. The proofs combine and extend recent developments in regularization by noise and in the Lp(Lq)-approach to stochastic PDEs, highlighting new connections between the two areas.","lang":"eng"}],"oa_version":"Submitted Version","department":[{"_id":"JuFi"}],"date_updated":"2023-12-18T07:53:45Z","ddc":["510"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12486"},{"doi":"10.1109/TIT.2023.3334032","date_published":"2023-11-16T00:00:00Z","date_created":"2023-12-10T23:01:00Z","day":"16","publication":"IEEE Transactions on Information Theory","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0018-9448"],"eissn":["1557-9654"]},"publication_status":"epub_ahead","year":"2023","month":"11","quality_controlled":"1","publisher":"IEEE","scopus_import":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2211.04408","open_access":"1"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We derive lower bounds on the maximal rates for multiple packings in high-dimensional Euclidean spaces. For any N > 0 and L ∈ Z ≥2 , a multiple packing is a set C of points in R n such that any point in R n lies in the intersection of at most L - 1 balls of radius √ nN around points in C . This is a natural generalization of the sphere packing problem. We study the multiple packing problem for both bounded point sets whose points have norm at most √ nP for some constant P > 0, and unbounded point sets whose points are allowed to be anywhere in R n . Given a well-known connection with coding theory, multiple packings can be viewed as the Euclidean analog of list-decodable codes, which are well-studied over finite fields. We derive the best known lower bounds on the optimal multiple packing density. This is accomplished by establishing an inequality which relates the list-decoding error exponent for additive white Gaussian noise channels, a quantity of average-case nature, to the list-decoding radius, a quantity of worst-case nature. We also derive novel bounds on the list-decoding error exponent for infinite constellations and closed-form expressions for the list-decoding error exponents for the power-constrained AWGN channel, which may be of independent interest beyond multiple packing."}],"title":"Multiple packing: Lower bounds via error exponents","department":[{"_id":"MaMo"}],"author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","orcid":"0000-0002-6465-6258","last_name":"Zhang"},{"first_name":"Shashank","last_name":"Vatedka","full_name":"Vatedka, Shashank"}],"article_processing_charge":"No","external_id":{"arxiv":["2211.04408"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory. IEEE, 2023. https://doi.org/10.1109/TIT.2023.3334032.","ista":"Zhang Y, Vatedka S. 2023. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory.","mla":"Zhang, Yihan, and Shashank Vatedka. “Multiple Packing: Lower Bounds via Error Exponents.” IEEE Transactions on Information Theory, IEEE, 2023, doi:10.1109/TIT.2023.3334032.","ama":"Zhang Y, Vatedka S. Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. 2023. doi:10.1109/TIT.2023.3334032","apa":"Zhang, Y., & Vatedka, S. (2023). Multiple packing: Lower bounds via error exponents. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2023.3334032","ieee":"Y. Zhang and S. Vatedka, “Multiple packing: Lower bounds via error exponents,” IEEE Transactions on Information Theory. IEEE, 2023.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory (2023)."},"date_updated":"2023-12-18T07:46:45Z","status":"public","article_type":"original","type":"journal_article","_id":"14665"},{"author":[{"full_name":"Hoffmann, Charlotte","orcid":"0000-0003-2027-5549","last_name":"Hoffmann","first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7"},{"last_name":"Hubáček","full_name":"Hubáček, Pavel","first_name":"Pavel"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"first_name":"Tomáš","full_name":"Krňák, Tomáš","last_name":"Krňák"}],"article_processing_charge":"No","title":"(Verifiable) delay functions from Lucas sequences","citation":{"mla":"Hoffmann, Charlotte, et al. “(Verifiable) Delay Functions from Lucas Sequences.” 21st International Conference on Theory of Cryptography, vol. 14372, Springer Nature, 2023, pp. 336–62, doi:10.1007/978-3-031-48624-1_13.","ama":"Hoffmann C, Hubáček P, Kamath C, Krňák T. (Verifiable) delay functions from Lucas sequences. In: 21st International Conference on Theory of Cryptography. Vol 14372. Springer Nature; 2023:336-362. doi:10.1007/978-3-031-48624-1_13","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Krňák, T. (2023). (Verifiable) delay functions from Lucas sequences. In 21st International Conference on Theory of Cryptography (Vol. 14372, pp. 336–362). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48624-1_13","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and T. Krňák, “(Verifiable) delay functions from Lucas sequences,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14372, pp. 336–362.","short":"C. Hoffmann, P. Hubáček, C. Kamath, T. Krňák, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 336–362.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Tomáš Krňák. “(Verifiable) Delay Functions from Lucas Sequences.” In 21st International Conference on Theory of Cryptography, 14372:336–62. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48624-1_13.","ista":"Hoffmann C, Hubáček P, Kamath C, Krňák T. 2023. (Verifiable) delay functions from Lucas sequences. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14372, 336–362."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"336-362","doi":"10.1007/978-3-031-48624-1_13","date_published":"2023-11-27T00:00:00Z","date_created":"2023-12-17T23:00:54Z","year":"2023","day":"27","publication":"21st International Conference on Theory of Cryptography","quality_controlled":"1","publisher":"Springer Nature","oa":1,"acknowledgement":"Home Theory of Cryptography Conference paper\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nDownload book PDF\r\nDownload book EPUB\r\nSimilar content being viewed by others\r\n\r\nSlider with three content items shown per slide. Use the Previous and Next buttons to navigate the slides or the slide controller buttons at the end to navigate through each slide.\r\nPrevious slide\r\nGeneric-Group Delay Functions Require Hidden-Order Groups\r\nChapter© 2020\r\n\r\nShifted powers in Lucas–Lehmer sequences\r\nArticle30 January 2019\r\n\r\nA New Class of Trapdoor Verifiable Delay Functions\r\nChapter© 2023\r\n\r\nWeak Pseudoprimality Associated with the Generalized Lucas Sequences\r\nChapter© 2022\r\n\r\nOn the Security of Time-Lock Puzzles and Timed Commitments\r\nChapter© 2020\r\n\r\nGeneration of full cycles by a composition of NLFSRs\r\nArticle08 March 2014\r\n\r\nCryptographically Strong de Bruijn Sequences with Large Periods\r\nChapter© 2013\r\n\r\nOpen Problems on With-Carry Sequence Generators\r\nChapter© 2014\r\n\r\nGenerically Speeding-Up Repeated Squaring Is Equivalent to Factoring: Sharp Thresholds for All Generic-Ring Delay Functions\r\nChapter© 2020\r\n\r\nNext slide\r\nGo to slide 1\r\nGo to slide 2\r\nGo to slide 3\r\n(Verifiable) Delay Functions from Lucas Sequences\r\nCharlotte Hoffmann, Pavel Hubáček, Chethan Kamath & Tomáš Krňák \r\nConference paper\r\nFirst Online: 27 November 2023\r\n83 Accesses\r\n\r\nPart of the Lecture Notes in Computer Science book series (LNCS,volume 14372)\r\n\r\nAbstract\r\nLucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\n\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\n\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.\r\n\r\nKeywords\r\nDelay functions\r\nVerifiable delay functions\r\nLucas sequences\r\nDownload conference paper PDF\r\n\r\n1 Introduction\r\nA verifiable delay function (VDF) \r\n is a function that satisfies two properties. First, it is a delay function, which means it must take a prescribed (wall) time T to compute f, irrespective of the amount of parallelism available. Second, it should be possible for anyone to quickly verify – say, given a short proof \r\n – the value of the function (even without resorting to parallelism), where by quickly we mean that the verification time should be independent of or significantly smaller than T (e.g., logarithmic in T). If we drop either of the two requirements, then the primitive turns out trivial to construct. For instance, for an appropriately chosen hash function h, the delay function \r\n defined by T-times iterated hashing of the input is a natural heuristic for an inherently sequential task which, however, seems hard to verify more efficiently than by recomputing. On the other hand, the identity function \r\n is trivial to verify but also easily computable. Designing a simple function satisfying the two properties simultaneously proved to be a nontrivial task.\r\n\r\nThe notion of VDFs was introduced in [31] and later formalised in [9]. In principle, since the task of constructing a VDF reduces to the task of incrementally-verifiable computation [9, 53], constructions of VDFs could leverage succinct non-interactive arguments of knowledge (SNARKs): take any sequentially-hard function f (for instance, iterated hashing) as the delay function and then use the SNARK on top of it as the mechanism for verifying the computation of the delay function. However, as discussed in [9], the resulting construction is not quite practical since we would rely on a general-purpose machinery of SNARKs with significant overhead.\r\n\r\nEfficient VDFs via Algebraic Delay Functions. VDFs have recently found interesting applications in design of blockchains [17], randomness beacons [43, 51], proofs of data replication [9], or short-lived zero-knowledge proofs and signatures [3]. Since efficiency is an important factor there, this has resulted in a flurry of constructions of VDFs that are tailored with application and practicality in mind. They rely on more algebraic, structured delay functions that often involve iterating an atomic operation so that one can resort to custom proof systems to achieve verifiability. These constructions involve a range of algebraic settings like the RSA or class groups [5, 8, 25, 42, 55], permutation polynomials over finite fields [9], isogenies of elliptic curves [21, 52] and, very recently, lattices [15, 28]. The constructions in [42, 55] are arguably the most practical and the mechanism that underlies their delay function is the same: carry out iterated squaring in groups of unknown order, like RSA groups [47] or class groups [12]. What distinguishes these two proposals is the way verification is carried out, i.e., how the underlying “proof of exponentiation” works: while Pietrzak [42] resorts to an LFKN-style recursive proof system [35], Wesolowski [55] uses a clever linear decomposition of the exponent.\r\n\r\nIterated Modular Squaring and Sequentiality. The delay function that underlies the VDFs in [5, 25, 42, 55] is the same, and its security relies on the conjectured sequential hardness of iterated squaring in a group of unknown order (suggested in the context of time-lock puzzles by Rivest, Shamir, and Wagner [48]). Given that the practically efficient VDFs all rely on the above single delay function, an immediate open problem is to identify additional sources of sequential hardness that are structured enough to support practically efficient verifiability.\r\n\r\n1.1 Our Approach to (Verifiable) Delay Functions\r\nIn this work, we study an alternative source of sequential hardness in the algebraic setting and use it to construct efficient verifiable delay functions. The sequentiality of our delay function relies on an atomic operation that is related to the computation of so-called Lucas sequences [29, 34, 57], explained next.\r\n\r\nLucas Sequences. A Lucas sequence is a constant-recursive integer sequence that satisfies the recurrence relation\r\n\r\nfor integers P and Q.Footnote1 Specifically, the Lucas sequences of integers \r\n and \r\n of the first and second type (respectively) are defined recursively as\r\n\r\nwith \r\n, and\r\n\r\nwith \r\n.\r\n\r\nThese sequences can be alternatively defined by the characteristic polynomial \r\n. Specifically, given the discriminant \r\n of the characteristic polynomial, one can alternatively compute the above sequences by performing operations in the extension field\r\n\r\nusing the identities\r\n\r\nwhere \r\n and its conjugate \r\n are roots of the characteristic polynomial. Since conjugation and exponentiation commute in the extension field (i.e., \r\n), computing the i-th terms of the two Lucas sequences over integers reduces to computing \r\n in the extension field, and vice versa.\r\n\r\nThe intrinsic connection between computing the terms in the Lucas sequences and that of exponentiation in the extension has been leveraged to provide alternative instantiations of public-key encryption schemes like RSA and ElGamal in terms of Lucas sequences [7, 30]. However, as we explain later, the corresponding underlying computational hardness assumptions are not necessarily equivalent.\r\n\r\nOverview of Our Delay Function. The delay function in [5, 25, 42, 55] is defined as the iterated squaring base x in a (safe) RSA groupFootnote2 modulo N:\r\n\r\nOur delay function is its analogue in the setting of Lucas sequences:\r\n\r\nAs mentioned above, computing \r\n can be carried out equivalently in the extension field \r\n using the known relationship to roots of the characteristic polynomial of the Lucas sequence. Thus, the delay function can be alternatively defined as\r\n\r\nNote that the atomic operation of our delay function is “doubling” the index of an element of the Lucas sequence modulo N (i.e., \r\n) or, equivalently, squaring in the extension field \r\n (as opposed to squaring in \r\n). Using the representation of \r\n as \r\n, squaring in \r\n can be expressed as a combination of squaring, multiplication and addition modulo N, since\r\n\r\n(1)\r\nSince \r\n is a group of unknown order (provided the factorization of N is kept secret), iterated squaring remains hard here. In fact, we show in Sect. 3.2 that iterated squaring in \r\n is at least as hard as iterated squaring for RSA moduli N. Moreover, we conjecture in Conjecture 1 that it is, in fact, strictly harder (also see discussion below on advantages of our approach).\r\n\r\nVerifying Modular Lucas Sequence. To obtain a VDF, we need to show how to efficiently verify our delay function. To this end, we show how to adapt the interactive proof of exponentiation from [42] to our setting, which then – via the Fiat-Shamir Transform [22] – yields the non-interactive verification algorithm.Footnote3 Thus, our main result is stated informally below.\r\n\r\nTheorem 1\r\n(Informally stated, see Theorem 2). Assuming sequential hardness of modular Lucas sequence, there exists statistically-sound VDF in the random-oracle model.\r\n\r\nHowever, the modification of Pietrzak’s protocol is not trivial and we have to overcome several hurdles that we face in this task, which we elaborate on in Sect. 1.2. We conclude this section with discussions about our results.\r\n\r\nAdvantage of Our Approach. Our main advantage is the reliance on a potentially weaker (sequential) hardness assumption while maintaining efficiency: we show in Sect. 3.2 that modular Lucas sequences are at least as sequentially-hard as the classical delay function given by iterated modular squaring [48]. Despite the linear recursive structure of Lucas sequences, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring (Conjecture 1). In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring. Even though both assumptions need the group order to be hidden, we believe that there is need for a nuanced analysis of sequential hardness assumptions in hidden order groups, especially because all current delay functions that provide sufficient structure for applications are based on iterated modular squaring. If the iterated modular squaring assumption is broken, our delay function is currently the only practical alternative in the RSA group.\r\n\r\nDelay Functions in Idealised Models. Recent works studied the relationship of group-theoretic (verifiable) delay functions to the hardness of factoring in idealised models such as the algebraic group model and the generic ring model [27, 50]. In the generic ring model, Rotem and Segev [50] showed the equivalence of straight-line delay functions in the RSA setting and factoring. Our construction gives rise to a straight-line delay function and, by their result, its sequentiality is equivalent to factoring for generic algorithms. However, their result holds only in the generic ring model and leaves the relationship between the two assumptions unresolved in the standard model.\r\n\r\nCompare this with the status of the RSA assumption and factoring. On one hand, we know that in the generic ring model, RSA and factoring are equivalent [2]. Yet, it is possible to rule out certain classes of reductions from factoring to RSA in the standard model [11]. Most importantly, despite the equivalence in the generic ring model, there is currently no reduction from factoring to RSA in the standard model and it remains one of the major open problems in number theory related to cryptography since the introduction of the RSA assumption.\r\n\r\nIn summary, speeding up iterated squaring by a non-generic algorithm could be possible (necessarily exploiting the representations of ring elements modulo N), while such an algorithm may not lead to a speed-up in the computation of modular Lucas sequences despite the result of Rotem and Segev [50].\r\n\r\n1.2 Technical Overview\r\nPietrzak’s VDF. Let \r\n be an RSA modulus where p and q are safe primes and let x be a random element from \r\n. At its core, Pietrzak’s VDF relies on the interactive protocol for the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and, in a round-by-round fashion, reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round, the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued till \r\n is obtained at which point the verifier simply checks whether \r\n using a single modular squaring.\r\n\r\nSince the challenges r are public, the protocol can be compiled into a non-interactive one using the Fiat-Shamir transform [22] and this yields a means to verify the delay function\r\n\r\nIt is worth pointing out that the choice of safe primes is crucial for proving soundness: in case the group has easy-to-find elements of small order then it becomes easy to break soundness (see, e.g., [10]).\r\n\r\nAdapting Pietrzak’s Protocol to Lucas Sequences. For a modulus \r\n and integers \r\n, recall that our delay function is defined as\r\n\r\nor equivalently\r\n\r\nfor the discriminant \r\n of the characteristic polynomial \r\n. Towards building a verification algorithm for this delay function, the natural first step is to design an interactive protocol for the statement\r\n\r\n“(N, P, Q, y, T) satisfies \r\n.”\r\n\r\nIt turns out that the interactive protocol from [42] can be adapted for this purpose. However, we encounter two technicalities in this process.\r\n\r\nDealing with elements of small order. The main problem that we face while designing our protocol is avoiding elements of small order. In the case of [42], this was accomplished by moving to the setting of signed quadratic residues [26] in which the sub-groups are all of large order. It is not clear whether a corresponding object exists for our algebraic setting. However, in an earlier draft of Pietrzak’s protocol [41], this problem was dealt with in a different manner: the prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by squaring it) with a guarantee that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nIn our setting, we cannot simply ask for the square root of the midpoint as the subgroup of \r\n we effectively work in has a different structure. Nevertheless, we can use a similar approach: for an appropriately chosen small a, we provide an a-th root of \r\n (instead of \r\n itself) to the prover in the beginning of the protocol. The prover then computes the whole sequence for \r\n. In the end, he has the a-th root of every term of the original sequence and he can recover any element of the original sequence by raising to the a-th power.\r\n\r\nSampling strong modulus. The second technicality is related to the first one. In order to ensure that we can use the above trick, we require a modulus where the small subgroups are reasonably small not only in the group \r\n but also in the extension \r\n. Thus the traditional sampling algorithms that are used to sample strong primes (e.g., [46]) are not sufficient for our purposes. However, sampling strong primes that suit our criteria can still be carried out efficiently as we show in the full version.\r\n\r\nComparing Our Technique with [8, 25]. The VDFs in [8, 25] are also inspired by [42] and, hence, faced the same problem of low-order elements. In [8], this is dealt with by amplifying the soundness at the cost of parallel repetition and hence larger proofs and extra computation. In [25], the number of repetitions of [8] is reduced significantly by introducing the following technique: The exponent of the initial instance is reduced by some parameter \r\n and at the end of an interactive phase, the verifier performs final exponentiation with \r\n, thereby weeding out potential false low-order elements in the claim. This technique differs from the approach taken in our work in the following ways: The technique from [25] works in arbitrary groups but it requires the parameter \r\n to be large and of a specific form. In particular, the VDF becomes more efficient when \r\n is larger than \r\n. In our protocol, we work in RSA groups whose modulus is the product of primes that satisfy certain conditions depending on a. This enables us to choose a parameter a that is smaller than a statistical security parameter and thereby makes the final exponentiation performed by the verifier much more efficient. Further, a can be any natural number, while \r\n must be set as powers of all small prime numbers up a certain bound in [25].\r\n\r\n1.3 More Related Work\r\nTimed Primitives. The notion of VDFs was introduced in [31] and later formalised in [9]. VDFs are closely related to the notions of time-lock puzzles [48] and proofs of sequential work [36]. Roughly speaking, a time-lock puzzle is a delay function that additionally allows efficient sampling of the output via a trapdoor. A proof of sequential work, on the other hand, is a delay “multi-function”, in the sense that the output is not necessarily unique. Constructions of time-lock puzzles are rare [6, 38, 48], and there are known limitations: e.g., that it cannot exist in the random-oracle model [36]. However, we know how to construct proofs of sequential work in the random-oracle model [1, 16, 19, 36].\r\n\r\nSince VDFs have found several applications, e.g., in the design of resource-efficient blockchains [17], randomness beacons [43, 51] and proof of data replication [9], there have been several constructions. Among them, the most notable are the iterated-squaring based construction from [8, 25, 42, 55], the permutation-polynomial based construction from [9], the isogenies-based construction from [13, 21, 52] and the construction from lattice problems [15, 28]. The constructions in [42, 55] are quite practical (see the survey [10]) and the VDF deployed in the cryptocurrency Chia is basically their construction adapted to the algebraic setting of class groups [17]. This is arguably the closest work to ours. On the other hand, the constructions from [21, 52], which work in the algebraic setting of isogenies of elliptic curves where no analogue of square and multiply is known, simply rely on “exponentiation”. Although, these constructions provide a certain form of quantum resistance, they are presently far from efficient. Freitag et al. [23] constructed VDFs from any sequentially hard function and polynomial hardness of learning with errors, the first from standard assumptions. The works of Cini, Lai, and Malavolta [15, 28] constructed the first VDF from lattice-based assumptions and conjectured it to be post-quantum secure.\r\n\r\nSeveral variants of VDFs have also been proposed. A VDF is said to be unique if the proof that is used for verification is unique [42]. Recently, Choudhuri et al. [5] constructed unique VDFs from the sequential hardness of iterated squaring in any RSA group and polynomial hardness of LWE. A VDF is tight [18] if the gap between simply computing the function and computing it with a proof is small. Yet another extension is a continuous VDF [20]. The feasibility of time-lock puzzles and proofs of sequential works were recently extended to VDFs. It was shown [50] that the latter requirement, i.e., working in a group of unknown order, is inherent in a black-box sense. It was shown in [18, 37] that there are barriers to constructing tight VDFs in the random-oracle model.\r\n\r\nVDFs also have surprising connection to complexity theory [14, 20, 33].\r\n\r\nWork Related to Lucas Sequences. Lucas sequences have long been studied in the context of number theory: see for example [45] or [44] for a survey of its applications to number theory. Its earliest application to cryptography can be traced to the \r\n factoring algorithm [56]. Constructive applications were found later thanks to the parallels with exponentiation. Several encryption and signature schemes were proposed, most notably the LUC family of encryption and signatures [30, 39]. It was later shown that some of these schemes can be broken or that the advantages it claimed were not present [7]. Other applications can be found in [32].\r\n\r\n2 Preliminaries\r\n2.1 Interactive Proof Systems\r\nInteractive Protocols. An interactive protocol consists of a pair \r\n of interactive Turing machines that are run on a common input \r\n. The first machine \r\n is the prover and is computationally unbounded. The second machine \r\n is the verifier and is probabilistic polynomial-time.\r\n\r\nIn an \r\n-round (i.e., \r\n-message) interactive protocol, in each round \r\n, first \r\n sends a message \r\n to \r\n and then \r\n sends a message \r\n to \r\n, where \r\n is a finite alphabet. At the end of the interaction, \r\n runs a (deterministic) Turing machine on input \r\n. The interactive protocol is public-coin if \r\n is a uniformly distributed random string in \r\n.\r\n\r\nInteractive Proof Systems. The notion of an interactive proof for a language L is due to Goldwasser, Micali and Rackoff [24].\r\n\r\nDefinition 1\r\nFor a function \r\n, an interactive protocol \r\n is an \r\n-statistically-sound interactive proof system for L if:\r\n\r\nCompleteness: For every \r\n, if \r\n interacts with \r\n on common input \r\n, then \r\n accepts with probability 1.\r\n\r\nSoundness: For every \r\n and every (computationally-unbounded) cheating prover strategy \r\n, the verifier \r\n accepts when interacting with \r\n with probability less than \r\n, where \r\n is called the soundness error.\r\n\r\n2.2 Verifiable Delay Functions\r\nWe adapt the definition of verifiable delay functions from [9] but we decouple the verifiability and sequentiality properties for clarity of exposition of our results. First, we present the definition of a delay function.\r\n\r\nDefinition 2\r\nA delay function \r\n consists of a triple of algorithms with the following syntax:\r\n\r\n:\r\n\r\nOn input a security parameter \r\n, the algorithm \r\n outputs public parameters \r\n.\r\n\r\n:\r\n\r\nOn input public parameters \r\n and a time parameter \r\n, the algorithm \r\n outputs a challenge x.\r\n\r\n:\r\n\r\nOn input a challenge pair (x, T), the (deterministic) algorithm \r\n outputs the value y of the delay function in time T.\r\n\r\nThe security property required of a delay function is sequential hardness as defined below.\r\n\r\nDefinition 3\r\n(Sequentiality). We say that a delay function \r\n satisfies the sequentiality property, if there exists an \r\n such that for all \r\n and for every adversary \r\n, where \r\n uses \r\n processors and runs in time \r\n, there exists a negligible function \r\n such that\r\n\r\nfigure a\r\nA few remarks about our definition of sequentiality are in order:\r\n\r\n1.\r\nWe require computing \r\n to be hard in less than T sequential steps even using any polynomially-bounded amount of parallelism and precomputation. Note that it is necessary to bound the amount of parallelism, as an adversary could otherwise break the underlying hardness assumption (e.g. hardness of factorization). Analogously, T should be polynomial in \r\n as, otherwise, breaking the underlying hardness assumptions becomes easier than computing \r\n itself for large values of T.\r\n\r\n2.\r\nAnother issue is what bound on the number of sequential steps of the adversary should one impose. For example, the delay function based on T repeated modular squarings can be computed in sequential time \r\n using polynomial parallelism [4]. Thus, one cannot simply bound the sequential time of the adversary by o(T). Similarly to [38], we adapt the \r\n bound for \r\n which, in particular, is asymptotically smaller than \r\n.\r\n\r\n3.\r\nWithout loss of generality, we assume that the size of \r\n is at least linear in n and the adversary A does not have to get the unary representation of the security parameter \r\n as its input.\r\n\r\nThe definition of verifiable delay function extends a delay function with the possibility to compute publicly-verifiable proofs of correctness of the output value.\r\n\r\nDefinition 4\r\nA delay function \r\n is a verifiable delay function if it is equipped with two additional algorithms \r\n and \r\n with the following syntax:\r\n\r\n:\r\n\r\nOn input public parameters and a challenge pair (x, T), the \r\n algorithm outputs \r\n, where \r\n is a proof that the output y is the output of \r\n.\r\n\r\n:\r\n\r\nOn input public parameters, a challenge pair (x, T), and an output/proof pair \r\n, the (deterministic) algorithm \r\n outputs either \r\n or \r\n.\r\n\r\nIn addition to sequentiality (inherited from the underlying delay function), the \r\n and \r\n algorithms must together satisfy correctness and (statistical) soundness as defined below.\r\n\r\nDefinition 5\r\n(Correctness). A verifiable delay function \r\n is correct if for all \r\n\r\nfigure b\r\nDefinition 6\r\n(Statistical soundness). A verifiable delay function \r\n is statistically sound if for every (computationally unbounded) malicious prover \r\n there exists a negligible function \r\n such that for all \r\n\r\nfigure c\r\n3 Delay Functions from Lucas Sequences\r\nIn this section, we propose a delay function based on Lucas sequences and prove its sequentiality assuming that iterated squaring in a group of unknown order is sequential (Sect. 3.1). Further, we conjecture (Sect. 3.2) that our delay function candidate is even more robust than its predecessor proposed by Rivest, Shamir, and Wagner [48]. Finally, we turn our delay function candidate into a verifiable delay function (Sect. 4).\r\n\r\n3.1 The Atomic Operation\r\nOur delay function is based on subsequences of Lucas sequences, whose indexes are powers of two. Below, we use \r\n to denote the set of non-negative integers.\r\n\r\nDefinition 7\r\nFor integers \r\n, the Lucas sequences \r\n and \r\n are defined for all \r\n as\r\n\r\nwith \r\n and \r\n, and\r\n\r\nwith \r\n and \r\n.\r\n\r\nWe define subsequences \r\n, respectively \r\n, of \r\n, respectively \r\n for all \r\n as\r\n\r\n(2)\r\nAlthough the value of \r\n depends on parameters (P, Q), we omit (P, Q) from the notation because these parameters will be always obvious from the context.\r\n\r\nThe underlying atomic operation for our delay function is\r\n\r\nThere are several ways to compute \r\n in T sequential steps, and we describe two of them below.\r\n\r\nAn Approach Based on Squaring in a Suitable Extension Ring. To compute the value \r\n, we can use the extension ring \r\n, where \r\n is the discriminant of the characteristic polynomial \r\n of the Lucas sequence. The characteristic polynomial f(z) has a root \r\n, and it is known that, for all \r\n, it holds that\r\n\r\nThus, by iterated squaring of \r\n, we can compute terms of our target subsequences. To get a better understanding of squaring in the extension ring, consider the representation of the root \r\n for some \r\n. Then,\r\n\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(3)\r\nAn Approach Based on Known Identities. Many useful identities for members of modular Lucas sequences are known, such as\r\n\r\n(4)\r\nSetting \r\n we get\r\n\r\n(5)\r\nThe above identities are not hard to derive (see, e.g., Lemma 12.5 in [40]). Indexes are doubled on each of application of the identities in Eq. (5), and, thus, for \r\n, we define an auxiliary sequence \r\n by \r\n. Using the identities in Eq. (5), we get recursive equations\r\n\r\n(6)\r\nThen, the atomic operation of our delay function can be interpreted as \r\n, defined for all \r\n as\r\n\r\n(7)\r\nAfter a closer inspection, the reader may have an intuition that an auxiliary sequence \r\n, which introduces a third state variable, is redundant. This intuition is indeed right. In fact, there is another easily derivable identity\r\n\r\n(8)\r\nwhich can be found, e.g., as Lemma 12.2 in [40]. On the other hand, Eq. (8) is quite interesting because it allows us to compute large powers of an element \r\n using two Lucas sequences. We use this fact in the security reduction in Sect. 3.2. Our construction of a delay function, denoted \r\n, is given in Fig. 1.\r\n\r\nFig. 1.\r\nfigure 1\r\nOur delay function candidate \r\n based on a modular Lucas sequence.\r\n\r\nFull size image\r\nOn the Discriminant D. Notice that whenever D is a quadratic residue modulo N, the value \r\n is an element of \r\n and hence \r\n. By definition, LCS.Gen generates a parameter D that is a quadratic residue with probability 1/4, so it might seem that in one fourth of the cases there is another approach to compute \r\n: find the element \r\n and then perform n sequential squarings in the group \r\n. However, it is well known that finding square roots of uniform elements in \r\n is equivalent to factoring the modulus N, so this approach is not feasible. We can therefore omit any restrictions on the discriminant D in the definition of our delay function LCS.\r\n\r\n3.2 Reduction from RSW Delay Function\r\nIn order to prove the sequentiality property (Definition 3) of our candidate \r\n, we rely on the standard conjecture of the sequentiality of the \r\n time-lock puzzles, implicitly stated in [48] as the underlying hardness assumption.\r\n\r\nDefinition 8\r\n(\r\n delay function). The \r\n delay function is defined as follows:\r\n\r\n: Samples two n-bit primes p and q and outputs \r\n.\r\n\r\n: Outputs an x sampled from the uniform distribution on \r\n.\r\n\r\n: Outputs \r\n.\r\n\r\nTheorem 2\r\nIf the \r\n delay function has the sequentiality property, then the \r\n delay function has the sequentiality property.\r\n\r\nProof\r\nSuppose there exists an adversary \r\n who contradicts the sequentiality of \r\n, where \r\n is a precomputation algorithm and \r\n is an online algorithm. We construct an adversary \r\n who contradicts the sequentiality of \r\n as follows:\r\n\r\nThe algorithm \r\n is defined identically to the algorithm \r\n.\r\n\r\nOn input \r\n, \r\n picks a P from the uniform distribution on \r\n, sets\r\n\r\nand it runs \r\n to compute \r\n. The algorithm \r\n computes \r\n using the identity in Eq. (8).\r\n\r\nNote that the input distribution for the algorithm \r\n produced by \r\n differs from the one produced by \r\n, because the \r\n generator samples Q from the uniform distribution on \r\n (instead of \r\n). However, this is not a problem since the size of \r\n is negligible compared to the size of \r\n, so the statistical distance between the distribution of D produced by \r\n and the distribution of D sampled by \r\n is negligible in the security parameter. Thus, except for a negligible multiplicative loss, the adversary \r\n attains the same success probability of breaking the sequentiality of \r\n as the probability of \r\n breaking the sequentiality of \r\n – a contradiction to the assumption of the theorem. \r\n\r\nWe believe that the converse implication to Theorem 2 is not true, i.e., that breaking the sequentiality of \r\n does not necessarily imply breaking the sequentiality of \r\n. Below, we state it as a conjecture.\r\n\r\nConjecture 1\r\nSequentiality of \r\n cannot be reduced to sequentiality of \r\n.\r\n\r\nOne reason why the above conjecture might be true is that, while the \r\n delay function is based solely only on multiplication in the group \r\n, our \r\n delay function uses the full arithmetic (addition and multiplication) of the commutative ring \r\n.\r\n\r\nOne way to support the conjecture would be to construct an algorithm that speeds up iterated squaring but is not immediately applicable to Lucas sequences. By [49] we know that this cannot be achieved by a generic algorithm. A non-generic algorithm that solves iterated squaring in time \r\n is presented in [4]. The main tool of their construction is the Explicit Chinese Remainder Theorem modulo N. However, a similiar theorem exists also for univariate polynomial rings, which suggests that a similar speed-up can be obtained for our delay function by adapting the techniques in [4] to our setting.\r\n\r\n4 VDF from Lucas Sequences\r\nIn Sect. 3.1 we saw different ways of computing the atomic operation of the delay function. Computing \r\n in the extension field seems to be the more natural and time and space effective approach. Furthermore, writing the atomic operation \r\n as \r\n is very clear, and, thus, we follow this approach throughout the rest of the paper.\r\n\r\n4.1 Structure of \r\nTo construct a VDF based on Lucas sequences, we use an algebraic extension\r\n\r\n(9)\r\nwhere N is an RSA modulus and \r\n. In this section, we describe the structure of the algebraic extension given in Expression (9). Based on our understanding of the structure of the above algebraic extension, we can conclude that using modulus N composed of safe primes (i.e., for all prime factors p of N, \r\n has a large prime divisor) is necessary but not sufficient condition for security of our construction. We specify some sufficient conditions on factors of N in the subsequent Sect. 4.2.\r\n\r\nFirst, we introduce some simplifying notation for quotient rings.\r\n\r\nDefinition 9\r\nFor \r\n and \r\n, we denote by \r\n the quotient ring \r\n, where (m, f(x)) denotes the ideal of the ring \r\n generated by m and f(x).\r\n\r\nObservation 1, below, allows us to restrict our analysis only to the structure of \r\n for prime \r\n.\r\n\r\nObservation 1\r\nLet \r\n be distinct primes, \r\n and \r\n. Then\r\n\r\nProof\r\nUsing the Chinese reminder theorem, we get\r\n\r\nas claimed. \r\n\r\nThe following lemma characterizes the structure of \r\n with respect to the discriminant of f. We use \r\n to denote the standard Legendre symbol.\r\n\r\nLemma 1\r\nLet \r\n and \r\n be a polynomial of degree 2 with the discriminant D. Then\r\n\r\nProof\r\nWe consider each case separately:\r\n\r\nIf \r\n, then f(x) is irreducible over \r\n and \r\n is a field with \r\n elements. Since \r\n is a finite field, \r\n is cyclic and contains \r\n elements.\r\n\r\nIf \r\n, then \r\n and f has some double root \r\n and it can be written as \r\n for some \r\n. Since the ring \r\n is isomorphic to the ring \r\n (consider the isomorphism \r\n), we can restrict ourselves to describing the structure of \r\n.\r\n\r\nWe will prove that the function \r\n,\r\n\r\nis an isomorphism. First, the polynomial \r\n is invertible if and only if \r\n (inverse is \r\n). For the choice \r\n, we have\r\n\r\nThus \r\n is onto. Second, \r\n is, in fact, a bijection, because\r\n\r\n(10)\r\nFinally, \r\n is a homomorphism, because\r\n\r\nIf \r\n, then f(x) has two roots \r\n. We have an isomorphism\r\n\r\nand \r\n. \r\n\r\n4.2 Strong Groups and Strong Primes\r\nTo achieve the verifiability property of our construction, we need \r\n to contain a strong subgroup (defined next) of order asymptotically linear in p. We remark that our definition of strong primes is stronger than the one by Rivest and Silverman [46].\r\n\r\nDefinition 10\r\n(Strong groups). For \r\n, we say that a non-trivial group \r\n is \r\n-strong, if the order of each non-trivial subgroup of \r\n is greater than \r\n.\r\n\r\nObservation 2\r\nIf \r\n and \r\n are \r\n-strong groups, then \r\n is a \r\n-strong group.\r\n\r\nIt can be seen from Lemma 1 that \r\n always contains groups of small order (e.g. \r\n). To avoid these, we descend into the subgroup of a-th powers of elements of \r\n. Below, we introduce the corresponding notation.\r\n\r\nDefinition 11\r\nFor an Abelian group \r\n and \r\n, we define the subgroup \r\n of \r\n in the multiplicative notation and \r\n in the additive notation.\r\n\r\nFurther, we show in Lemma 2 below that \r\n-strong primality (defined next) is a sufficient condition for \r\n to be a \r\n-strong group.\r\n\r\nDefinition 12\r\n(Strong primes). Let \r\n and \r\n. We say that p is a \r\n-strong prime, if \r\n and there exists \r\n, \r\n, such that \r\n and every prime factor of W is greater than \r\n.\r\n\r\nSince a is a public parameter in our setup, super-polynomial a could reveal partial information about the factorization of N. However, we could allow a to be polynomial in \r\n while maintaining hardness of factoring N.Footnote4 For the sake of simplicity of Definition 12, we rather use stronger condition \r\n. The following simple observation will be useful for proving Lemma 2.\r\n\r\nObservation 3\r\nFor \r\n.\r\n\r\nLemma 2\r\nLet p be a \r\n-strong prime and \r\n be a quadratic polynomial. Then, \r\n is a \r\n-strong group.\r\n\r\nProof\r\nFrom definition of the strong primes, there exists \r\n, whose factors are bigger than \r\n and \r\n. We denote \r\n a factor of W. Applying Observation 3 to Lemma 1, we get\r\n\r\nIn particular, we used above the fact that Observation 2 implies that \r\n as explained next. Since \r\n, all divisors of \r\n are divisors of aW. By definition of a and W in Definition 12, we also have that \r\n, which implies that any factor of \r\n divides either a or W, but not both. When we divide \r\n by all the common divisors with a, only the common divisors with W are left, which implies \r\n. The proof of the lemma is now completed by Observation 2.\r\n\r\nCorollary 1\r\nLet p be a \r\n-strong prime, q be a \r\n-strong prime, \r\n, \r\n, \r\n and \r\n. Then \r\n is \r\n-strong.\r\n\r\n4.3 Our Interactive Protocol\r\nOur interactive protocol is formally described in Fig. 3. To understand this protocol, we first recall the outline of Pietrzak’s interactive protocol from Sect. 1.2 and then highlight the hurdles. Let \r\n be an RSA modulus where p and q are strong primes and let x be a random element from \r\n. The interactive protocol in [42] allows a prover to convince the verifier of the statement\r\n\r\n“(N, x, y, T) satisfies \r\n”.\r\n\r\nThe protocol is recursive and in a round-by-round fashion reduces the claim to a smaller statement by halving the time parameter. To be precise, in each round the (honest) prover sends the “midpoint” \r\n of the current statement to the verifier and they together reduce the statement to\r\n\r\n“\r\n satisfies \r\n”,\r\n\r\nwhere \r\n and \r\n for a random challenge r. This is continued until \r\n is obtained at which point the verifier simply checks whether \r\n.\r\n\r\nThe main problem, we face while designing our protocol is ensuring that the verifier can check whether \r\n sent by prover lies in an appropriate subgroup of \r\n. In the first draft of Pietrzak’s protocol [41], prover sends a square root of \r\n, from which the original \r\n can be recovered easily (by simply squaring it) with a guarantee, that the result lies in a group of quadratic residues \r\n. Notice that the prover knows the square root of \r\n, because it is just a previous term in the sequence he computed.\r\n\r\nUsing Pietrzak’s protocol directly for our delay function would require computing a-th roots in RSA group for some arbitrary a. Since this is a computationally hard problem, we cannot use the same trick. In fact, the VDF construction of Wesolowski [54] is based on similar hardness assumption.\r\n\r\nWhile Pietrzak shifted from \r\n to the group of signed quadratic residues \r\n in his following paper [42] to get unique proofs, we resort to his old idea of ‘squaring a square root’ and generalise it.\r\n\r\nThe high level idea is simple. First, on input \r\n, prover computes the sequence \r\n. Next, during the protocol, verifier maps all elements sent by the prover by homomorphism\r\n\r\n(11)\r\ninto the target strong group \r\n. This process is illustrated in Fig. 2. Notice that the equality \r\n for the original sequence implies the equality \r\n for the mapped sequence \r\n.\r\n\r\nFig. 2.\r\nfigure 2\r\nIllustration of our computation of the iterated squaring using the a-th root of \r\n. Horizontal arrows are \r\n and diagonal arrows are \r\n.\r\n\r\nFull size image\r\nRestriction to Elements of \r\n. Mapping Eq. (11) introduces a new technical difficulty. Since \r\n is not injective, we narrow the domain inputs, for which the output of our VDF is verifiable, from \r\n to \r\n. Furthermore, the only way to verify that a certain x is an element of \r\n is to get an a-th root of x and raise it to the ath power. So we have to represent elements of \r\n by elements of \r\n anyway. To resolve these two issues, we introduce a non-unique representation of elements of \r\n.\r\n\r\nDefinition 13\r\nFor \r\n and \r\n, we denote \r\n (an element of \r\n) by [x]. Since this representation of \r\n is not unique, we define an equality relation by\r\n\r\nWe will denote by tilde () the elements that were already powered to the a by a verifier (i.e. ). Thus tilded variables verifiably belong to the target group \r\n.\r\n\r\nIn the following text, the goal of the brackets notation in Definition 13 is to distinguish places where the equality means the equality of elements of \r\n from those places, where the equality holds up to \r\n. A reader can also see the notation in Definition 13 as a concrete representation of elements of a factor group \r\n.\r\n\r\nOur security reduction 2 required the delay function to operate everywhere on \r\n. This is not a problem if the \r\n algorithm is modified to output the set \r\n.\r\n\r\nFig. 3.\r\nfigure 3\r\nOur Interactive Protocol for \r\n.\r\n\r\nFull size image\r\n4.4 Security\r\nRecall here that \r\n is \r\n-strong group, so there exist\r\n\r\n and \r\n such that\r\n\r\n(12)\r\nDefinition 14\r\nFor \r\n and \r\n, we define \r\n as i-th coordinate of \r\n, where \r\n is the isomorphism given by Eq. (12).\r\n\r\nLemma 3\r\nLet \r\n and \r\n. If \r\n, then\r\n\r\n\t(13)\r\nProof\r\nFix \r\n, \r\n and y. Let some \r\n satisfy\r\n\r\n(14)\r\nUsing notation from Definition 14, we rewrite Eq. (14) as a set of equations\r\n\r\nFor every \r\n, by reordering the terms, the j-th equation becomes\r\n\r\n(15)\r\nIf \r\n, then \r\n. Further for every \r\n. It follows that \r\n. Putting these two equations together gives us \r\n, which contradicts our assumption \r\n.\r\n\r\nIt follows that there exists \r\n such that\r\n\r\n(16)\r\nThereafter there exists \r\n such that \r\n divides \r\n and\r\n\r\n(17)\r\nFurthermore, from Eq. (15), \r\n divides \r\n. Finally, dividing eq. Eq. (15) by \r\n, we get that r is determined uniquely (\r\n),\r\n\r\nUsing the fact that \r\n, this uniqueness of r upper bounds number of \r\n, such that Eq. (14) holds, to one. It follows that the probability that Eq. (14) holds for r chosen randomly from the uniform distribution over \r\n is less than \r\n. \r\n\r\nCorollary 2\r\nThe halving protocol will turn an invalid input tuple (i.e. \r\n) into a valid output tuple (i.e. \r\n) with probability less than \r\n.\r\n\r\nTheorem 3\r\nFor any computationally unbounded prover who submits anything other than \r\n such that \r\n in phase 2 of the protocol, the soundness error is upper-bounded by \r\n\r\nProof\r\nIn each round of the protocol, T decreases to \r\n. It follows that the number of rounds of the halving protocol before reaching \r\n is upper bounded by \r\n.\r\n\r\nIf the verifier accepts the solution tuple \r\n in the last round, then the equality \r\n must hold. It follows that the initial inequality must have turned into equality in some round of the halving protocol. By Lemma 3, the probability of this event is bounded by \r\n. Finally, using the union bound for all rounds, we obtain the upper bound (\r\n. \r\n\r\n4.5 Our VDF\r\nAnalogously to the VDF of Pietrzak [42], we compile our public-coin interactive proof given in Fig. 3 into a VDF using the Fiat-Shamir heuristic. The complete construction is given in Fig. 4. For ease of exposition, we assume that the time parameter T is always a power of two.\r\n\r\nFig. 4.\r\nfigure 4\r\n based on Lucas sequences\r\n\r\nFull size image\r\nAs discussed in Sect. 4.3, it is crucial for the security of the protocol that the prover computes a sequence of powers of the a-th root of the challenge and the resulting value (as well as the intermediate values) received from the prover is lifted to the appropriate group by raising it to the a-th power. We use the tilde notation in Fig. 4 in order to denote elements on the sequence relative to the a-th root.\r\n\r\nNote that, by the construction, the output of our VDF is the \r\n-th power of the root of the characteristic polynomial for Lucas sequence with parameters P and Q. Therefore, the value of the delay function implicitly corresponds to the \r\n-th term of the Lucas sequence.\r\n\r\nTheorem 4\r\nLet \r\n be the statistical security parameter. The \r\n VDF defined in Fig. 4 is correct and statistically-sound with a negligible soundness error if \r\n is modelled as a random oracle, against any adversary that makes \r\n oracle queries.\r\n\r\nProof\r\nThe correctness follows directly by construction.\r\n\r\nTo prove its statistical soundness, we proceed in a similar way to [42]. We cannot apply Fiat-Shamir transformation directly, because our protocol does not have constant number of rounds, thus we use Fiat-Shamir heuristic to each round separately.\r\n\r\nFirst, we use a random oracle as the \r\n function. Second, if a malicious prover computed a proof accepted by verifier for some tuple \r\n such that\r\n\r\n(19)\r\nthen he must have succeeded in turning inequality from Eq. (19) into equality in some round. By Lemma 3, probability of such a flipping is bounded by \r\n. Every such an attempt requires one query to random oracle. Using a union bound, it follows that the probability that a malicious prover who made q queries to random oracle succeeds in flipping initial inequality into equality in some round is upper-bounded by \r\n.\r\n\r\nSince q is \r\n, \r\n is a negligible function and thus the soundness error is negligible. \r\n\r\nNotes\r\n1.\r\nNote that integer sequences like Fibonacci numbers and Mersenne numbers are special cases of Lucas sequences.\r\n\r\n2.\r\nThe choice of modulus N is said to be safe if \r\n for safe primes \r\n and \r\n, where \r\n and \r\n are also prime.\r\n\r\n3.\r\nFurther, using the ideas from [14, 20], it is possible to construct so-called continuous VDFs from Lucas sequences.\r\n\r\n4.\r\nSince we set a to be at most polynomial in \r\n, its is possible to go over all possible candidate values for a in time polynomial in \r\n. 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Gaz. 83, 173 (1999)\r\n\r\nCrossRef\r\n \r\nGoogle Scholar\r\n \r\n\r\nDownload references\r\n\r\nAcknowledgements\r\nWe thank Krzysztof Pietrzak and Alon Rosen for several fruitful discussions about this work and the anonymous reviewers of SCN 2022 and TCC 2023 for valuable suggestions.\r\n\r\nPavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), by the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, by the European Research Council (ERC) under the European Union’s Horizon Europe research and innovation programme (grant agreement No. 101042417, acronym SPP), and by ISF grant 1789/19.","department":[{"_id":"KrPi"}],"date_updated":"2023-12-18T09:00:00Z","type":"conference","conference":{"end_date":"2023-12-02","location":"Taipei, Taiwan","start_date":"2023-11-29","name":"TCC: Theory of Cryptography"},"status":"public","_id":"14693","volume":14372,"publication_identifier":{"isbn":["9783031486234"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2023/1404"}],"month":"11","intvolume":" 14372","abstract":[{"text":"Lucas sequences are constant-recursive integer sequences with a long history of applications in cryptography, both in the design of cryptographic schemes and cryptanalysis. In this work, we study the sequential hardness of computing Lucas sequences over an RSA modulus.\r\nFirst, we show that modular Lucas sequences are at least as sequentially hard as the classical delay function given by iterated modular squaring proposed by Rivest, Shamir, and Wagner (MIT Tech. Rep. 1996) in the context of time-lock puzzles. Moreover, there is no obvious reduction in the other direction, which suggests that the assumption of sequential hardness of modular Lucas sequences is strictly weaker than that of iterated modular squaring. In other words, the sequential hardness of modular Lucas sequences might hold even in the case of an algorithmic improvement violating the sequential hardness of iterated modular squaring.\r\nSecond, we demonstrate the feasibility of constructing practically-efficient verifiable delay functions based on the sequential hardness of modular Lucas sequences. Our construction builds on the work of Pietrzak (ITCS 2019) by leveraging the intrinsic connection between the problem of computing modular Lucas sequences and exponentiation in an appropriate extension field.","lang":"eng"}],"oa_version":"Preprint"},{"date_updated":"2023-12-18T08:36:51Z","department":[{"_id":"KrPi"}],"_id":"14691","conference":{"name":"TCC: Theory of Cryptography","location":"Taipei, Taiwan","end_date":"2023-12-02","start_date":"2023-11-29"},"type":"conference","status":"public","publication_status":"published","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031486203"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"volume":14371,"abstract":[{"text":"Continuous Group-Key Agreement (CGKA) allows a group of users to maintain a shared key. It is the fundamental cryptographic primitive underlying group messaging schemes and related protocols, most notably TreeKEM, the underlying key agreement protocol of the Messaging Layer Security (MLS) protocol, a standard for group messaging by the IETF. CKGA works in an asynchronous setting where parties only occasionally must come online, and their messages are relayed by an untrusted server. The most expensive operation provided by CKGA is that which allows for a user to refresh their key material in order to achieve forward secrecy (old messages are secure when a user is compromised) and post-compromise security (users can heal from compromise). One caveat of early CGKA protocols is that these update operations had to be performed sequentially, with any user wanting to update their key material having had to receive and process all previous updates. Late versions of TreeKEM do allow for concurrent updates at the cost of a communication overhead per update message that is linear in the number of updating parties. This was shown to be indeed necessary when achieving PCS in just two rounds of communication by [Bienstock et al. TCC’20].\r\nThe recently proposed protocol CoCoA [Alwen et al. Eurocrypt’22], however, shows that this overhead can be reduced if PCS requirements are relaxed, and only a logarithmic number of rounds is required. The natural question, thus, is whether CoCoA is optimal in this setting.\r\nIn this work we answer this question, providing a lower bound on the cost (concretely, the amount of data to be uploaded to the server) for CGKA protocols that heal in an arbitrary k number of rounds, that shows that CoCoA is very close to optimal. Additionally, we extend CoCoA to heal in an arbitrary number of rounds, and propose a modification of it, with a reduced communication cost for certain k.\r\nWe prove our bound in a combinatorial setting where the state of the protocol progresses in rounds, and the state of the protocol in each round is captured by a set system, each set specifying a set of users who share a secret key. We show this combinatorial model is equivalent to a symbolic model capturing building blocks including PRFs and public-key encryption, related to the one used by Bienstock et al.\r\nOur lower bound is of order k•n1+1/(k-1)/log(k), where 2≤k≤log(n) is the number of updates per user the protocol requires to heal. This generalizes the n2 bound for k=2 from Bienstock et al.. This bound almost matches the k⋅n1+2/(k-1) or k2⋅n1+1/(k-1) efficiency we get for the variants of the CoCoA protocol also introduced in this paper.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://eprint.iacr.org/2023/1123","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 14371","month":"11","citation":{"mla":"Auerbach, Benedikt, et al. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 271–300, doi:10.1007/978-3-031-48621-0_10.","ama":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:271-300. doi:10.1007/978-3-031-48621-0_10","apa":"Auerbach, B., Cueto Noval, M., Pascual Perez, G., & Pietrzak, K. Z. (2023). On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 271–300). Taipei, Taiwan: Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_10","short":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, K.Z. Pietrzak, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 271–300.","ieee":"B. Auerbach, M. Cueto Noval, G. Pascual Perez, and K. Z. Pietrzak, “On the cost of post-compromise security in concurrent Continuous Group-Key Agreement,” in 21st International Conference on Theory of Cryptography, Taipei, Taiwan, 2023, vol. 14371, pp. 271–300.","chicago":"Auerbach, Benedikt, Miguel Cueto Noval, Guillermo Pascual Perez, and Krzysztof Z Pietrzak. “On the Cost of Post-Compromise Security in Concurrent Continuous Group-Key Agreement.” In 21st International Conference on Theory of Cryptography, 14371:271–300. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_10.","ista":"Auerbach B, Cueto Noval M, Pascual Perez G, Pietrzak KZ. 2023. On the cost of post-compromise security in concurrent Continuous Group-Key Agreement. 21st International Conference on Theory of Cryptography. TCC: Theory of Cryptography, LNCS, vol. 14371, 271–300."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","last_name":"Auerbach","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt"},{"first_name":"Miguel","id":"ffc563a3-f6e0-11ea-865d-e3cce03d17cc","last_name":"Cueto Noval","full_name":"Cueto Noval, Miguel"},{"id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","first_name":"Guillermo","orcid":"0000-0001-8630-415X","full_name":"Pascual Perez, Guillermo","last_name":"Pascual Perez"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"}],"title":"On the cost of post-compromise security in concurrent Continuous Group-Key Agreement","year":"2023","publication":"21st International Conference on Theory of Cryptography","day":"27","page":"271-300","date_created":"2023-12-17T23:00:53Z","date_published":"2023-11-27T00:00:00Z","doi":"10.1007/978-3-031-48621-0_10","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"article_processing_charge":"No","author":[{"full_name":"Auerbach, Benedikt","orcid":"0000-0002-7553-6606","last_name":"Auerbach","first_name":"Benedikt","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425"},{"orcid":"0000-0003-2027-5549","full_name":"Hoffmann, Charlotte","last_name":"Hoffmann","first_name":"Charlotte","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7"},{"last_name":"Pascual Perez","full_name":"Pascual Perez, Guillermo","orcid":"0000-0001-8630-415X","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87"}],"title":"Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing","citation":{"mla":"Auerbach, Benedikt, et al. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” 21st International Conference on Theory of Cryptography, vol. 14371, Springer Nature, 2023, pp. 301–30, doi:10.1007/978-3-031-48621-0_11.","ieee":"B. Auerbach, C. Hoffmann, and G. Pascual Perez, “Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing,” in 21st International Conference on Theory of Cryptography, 2023, vol. 14371, pp. 301–330.","short":"B. Auerbach, C. Hoffmann, G. Pascual Perez, in:, 21st International Conference on Theory of Cryptography, Springer Nature, 2023, pp. 301–330.","ama":"Auerbach B, Hoffmann C, Pascual Perez G. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In: 21st International Conference on Theory of Cryptography. Vol 14371. Springer Nature; 2023:301-330. doi:10.1007/978-3-031-48621-0_11","apa":"Auerbach, B., Hoffmann, C., & Pascual Perez, G. (2023). Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. In 21st International Conference on Theory of Cryptography (Vol. 14371, pp. 301–330). Springer Nature. https://doi.org/10.1007/978-3-031-48621-0_11","chicago":"Auerbach, Benedikt, Charlotte Hoffmann, and Guillermo Pascual Perez. “Generic-Group Lower Bounds via Reductions between Geometric-Search Problems: With and without Preprocessing.” In 21st International Conference on Theory of Cryptography, 14371:301–30. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-48621-0_11.","ista":"Auerbach B, Hoffmann C, Pascual Perez G. 2023. Generic-group lower bounds via reductions between geometric-search problems: With and without preprocessing. 21st International Conference on Theory of Cryptography. , LNCS, vol. 14371, 301–330."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"301-330","date_created":"2023-12-17T23:00:54Z","doi":"10.1007/978-3-031-48621-0_11","date_published":"2023-11-27T00:00:00Z","year":"2023","publication":"21st International Conference on Theory of Cryptography","day":"27","oa":1,"publisher":"Springer Nature","quality_controlled":"1","department":[{"_id":"KrPi"}],"date_updated":"2023-12-18T09:17:03Z","type":"conference","status":"public","_id":"14692","volume":14371,"publication_status":"published","publication_identifier":{"isbn":["9783031486203"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2023/808","open_access":"1"}],"scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 14371","month":"11","abstract":[{"text":"The generic-group model (GGM) aims to capture algorithms working over groups of prime order that only rely on the group operation, but do not exploit any additional structure given by the concrete implementation of the group. In it, it is possible to prove information-theoretic lower bounds on the hardness of problems like the discrete logarithm (DL) or computational Diffie-Hellman (CDH). Thus, since its introduction, it has served as a valuable tool to assess the concrete security provided by cryptographic schemes based on such problems. A work on the related algebraic-group model (AGM) introduced a method, used by many subsequent works, to adapt GGM lower bounds for one problem to another, by means of conceptually simple reductions.\r\nIn this work, we propose an alternative approach to extend GGM bounds from one problem to another. Following an idea by Yun [EC15], we show that, in the GGM, the security of a large class of problems can be reduced to that of geometric search-problems. By reducing the security of the resulting geometric-search problems to variants of the search-by-hypersurface problem, for which information theoretic lower bounds exist, we give alternative proofs of several results that used the AGM approach.\r\nThe main advantage of our approach is that our reduction from geometric search-problems works, as well, for the GGM with preprocessing (more precisely the bit-fixing GGM introduced by Coretti, Dodis and Guo [Crypto18]). As a consequence, this opens up the possibility of transferring preprocessing GGM bounds from one problem to another, also by means of simple reductions. Concretely, we prove novel preprocessing bounds on the hardness of the d-strong discrete logarithm, the d-strong Diffie-Hellman inversion, and multi-instance CDH problems, as well as a large class of Uber assumptions. Additionally, our approach applies to Shoup’s GGM without additional restrictions on the query behavior of the adversary, while the recent works of Zhang, Zhou, and Katz [AC22] and Zhandry [Crypto22] highlight that this is not the case for the AGM approach.","lang":"eng"}],"oa_version":"Preprint"},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"publication_status":"published","issue":"20","volume":108,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Generalized multifractality characterizes system size dependence of pure scaling local observables at Anderson transitions in all 10 symmetry classes of disordered systems. Recently, the concept of generalized multifractality has been extended to boundaries of critical disordered noninteracting systems. Here we study the generalized boundary multifractality in the presence of electron-electron interaction, focusing on the spin quantum Hall symmetry class (class C). Employing the two-loop renormalization group analysis within the Finkel'stein nonlinear sigma model, we compute the anomalous dimensions of the pure scaling operators located at the boundary of the system. We find that generalized boundary multifractal exponents are twice larger than their bulk counterparts. Exact symmetry relations between generalized boundary multifractal exponents in the case of noninteracting systems are explicitly broken by the interaction."}],"month":"11","intvolume":" 108","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2308.16852","open_access":"1"}],"date_updated":"2023-12-18T08:45:28Z","department":[{"_id":"MaSe"}],"_id":"14690","status":"public","type":"journal_article","article_type":"original","day":"15","publication":"Physical Review B","year":"2023","doi":"10.1103/PhysRevB.108.205429","date_published":"2023-11-15T00:00:00Z","date_created":"2023-12-17T23:00:53Z","acknowledgement":"The authors are grateful to J. Karcher and A. Mirlin for collaboration on the related project. We thank I. Gruzberg and A. Mirlin for useful discussions and comments. I.S.B. is grateful to M. Parfenov and P. Ostrovsky for collaboration on the related project. The research was supported by Russian Science Foundation (Grant No. 22-42-04416).","publisher":"American Physical Society","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Babkin S, Burmistrov I. 2023. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 108(20), 205429.","chicago":"Babkin, Serafim, and I Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B. American Physical Society, 2023. https://doi.org/10.1103/PhysRevB.108.205429.","ama":"Babkin S, Burmistrov I. Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. 2023;108(20). doi:10.1103/PhysRevB.108.205429","apa":"Babkin, S., & Burmistrov, I. (2023). Boundary multifractality in the spin quantum Hall symmetry class with interaction. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.108.205429","ieee":"S. Babkin and I. Burmistrov, “Boundary multifractality in the spin quantum Hall symmetry class with interaction,” Physical Review B, vol. 108, no. 20. American Physical Society, 2023.","short":"S. Babkin, I. Burmistrov, Physical Review B 108 (2023).","mla":"Babkin, Serafim, and I. Burmistrov. “Boundary Multifractality in the Spin Quantum Hall Symmetry Class with Interaction.” Physical Review B, vol. 108, no. 20, 205429, American Physical Society, 2023, doi:10.1103/PhysRevB.108.205429."},"title":"Boundary multifractality in the spin quantum Hall symmetry class with interaction","author":[{"first_name":"Serafim","id":"41e64307-6672-11ee-b9ad-cc7a0075a479","last_name":"Babkin","orcid":"0009-0003-7382-8036","full_name":"Babkin, Serafim"},{"last_name":"Burmistrov","full_name":"Burmistrov, I","first_name":"I"}],"article_processing_charge":"No","external_id":{"arxiv":["2308.16852"]},"article_number":"205429"},{"pmid":1,"oa_version":"None","scopus_import":"1","month":"12","intvolume":" 55","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":55,"issue":"12","_id":"14689","article_type":"letter_note","type":"journal_article","status":"public","date_updated":"2023-12-18T08:51:38Z","department":[{"_id":"MaRo"}],"quality_controlled":"1","publisher":"Springer Nature","year":"2023","day":"01","publication":"Nature Genetics","page":"2053-2055","date_published":"2023-12-01T00:00:00Z","doi":"10.1038/s41588-023-01595-5","date_created":"2023-12-17T23:00:53Z","citation":{"ama":"Ing-Simmons E, Machnik NN, Vaquerizas JM. 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Calvo, Larry A. Curtiss, Daniel Dewar, James H. J. Ellison, Xiangwen Gao, Clare P. Grey, et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3fd90059b.","ista":"Attard GA, Calvo EJ, Curtiss LA, Dewar D, Ellison JHJ, Gao X, Grey CP, Hardwick LJ, Horwitz G, Janek J, Johnson LR, Jordan JW, Matsuda S, Mondal S, Neale AR, Ortiz-Vitoriano N, Temprano I, Vailaya G, Wachsman ED, Wang H-H, Wu Y, Ye S. 2023. Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions.","mla":"Attard, Gary A., et al. “Materials for Stable Metal–Oxygen Battery Cathodes: General Discussion.” Faraday Discussions, Royal Society of Chemistry, 2023, doi:10.1039/d3fd90059b.","short":"G.A. Attard, E.J. Calvo, L.A. Curtiss, D. Dewar, J.H.J. Ellison, X. Gao, C.P. Grey, L.J. Hardwick, G. Horwitz, J. Janek, L.R. Johnson, J.W. Jordan, S. Matsuda, S. Mondal, A.R. Neale, N. Ortiz-Vitoriano, I. Temprano, G. Vailaya, E.D. Wachsman, H.-H. Wang, Y. Wu, S. Ye, Faraday Discussions (2023).","ieee":"G. A. Attard et al., “Materials for stable metal–oxygen battery cathodes: general discussion,” Faraday Discussions. Royal Society of Chemistry, 2023.","apa":"Attard, G. A., Calvo, E. J., Curtiss, L. A., Dewar, D., Ellison, J. H. J., Gao, X., … Ye, S. (2023). Materials for stable metal–oxygen battery cathodes: general discussion. Faraday Discussions. Royal Society of Chemistry. https://doi.org/10.1039/d3fd90059b","ama":"Attard GA, Calvo EJ, Curtiss LA, et al. Materials for stable metal–oxygen battery cathodes: general discussion. 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J."},{"full_name":"Gao, Xiangwen","last_name":"Gao","first_name":"Xiangwen"},{"last_name":"Grey","full_name":"Grey, Clare P.","first_name":"Clare P."},{"full_name":"Hardwick, Laurence J.","last_name":"Hardwick","first_name":"Laurence J."},{"first_name":"Gabriela","full_name":"Horwitz, Gabriela","last_name":"Horwitz"},{"first_name":"Juergen","full_name":"Janek, Juergen","last_name":"Janek"},{"full_name":"Johnson, Lee R.","last_name":"Johnson","first_name":"Lee R."},{"first_name":"Jack W.","last_name":"Jordan","full_name":"Jordan, Jack W."},{"first_name":"Shoichi","full_name":"Matsuda, Shoichi","last_name":"Matsuda"},{"full_name":"Mondal, Soumyadip","last_name":"Mondal","first_name":"Soumyadip","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48"},{"full_name":"Neale, Alex R.","last_name":"Neale","first_name":"Alex R."},{"full_name":"Ortiz-Vitoriano, Nagore","last_name":"Ortiz-Vitoriano","first_name":"Nagore"},{"first_name":"Israel","full_name":"Temprano, Israel","last_name":"Temprano"},{"first_name":"Ganesh","last_name":"Vailaya","full_name":"Vailaya, Ganesh"},{"last_name":"Wachsman","full_name":"Wachsman, Eric D.","first_name":"Eric D."},{"full_name":"Wang, Hsien-Hau","last_name":"Wang","first_name":"Hsien-Hau"},{"first_name":"Yiying","full_name":"Wu, Yiying","last_name":"Wu"},{"last_name":"Ye","full_name":"Ye, Shen","first_name":"Shen"}],"_id":"14702","keyword":["Physical and Theoretical Chemistry"],"status":"public","type":"journal_article","article_type":"review"},{"department":[{"_id":"MiSi"}],"file_date_updated":"2023-09-25T08:22:58Z","ddc":["570"],"date_updated":"2023-12-21T14:30:01Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14360","related_material":{"record":[{"id":"14697","status":"public","relation":"dissertation_contains"}]},"volume":14,"language":[{"iso":"eng"}],"file":[{"file_size":2725421,"date_updated":"2023-09-25T08:22:58Z","creator":"dernst","file_name":"2023_NatureComm_Sitarska.pdf","date_created":"2023-09-25T08:22:58Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"ad670e3b3c64fc585675948370f6b149","file_id":"14365"}],"publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"intvolume":" 14","month":"09","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"To navigate through diverse tissues, migrating cells must balance persistent self-propelled motion with adaptive behaviors to circumvent obstacles. We identify a curvature-sensing mechanism underlying obstacle evasion in immune-like cells. Specifically, we propose that actin polymerization at the advancing edge of migrating cells is inhibited by the curvature-sensitive BAR domain protein Snx33 in regions with inward plasma membrane curvature. The genetic perturbation of this machinery reduces the cells’ capacity to evade obstructions combined with faster and more persistent cell migration in obstacle-free environments. Our results show how cells can read out their surface topography and utilize actin and plasma membrane biophysics to interpret their environment, allowing them to adaptively decide if they should move ahead or turn away. On the basis of our findings, we propose that the natural diversity of BAR domain proteins may allow cells to tune their curvature sensing machinery to match the shape characteristics in their environment."}],"title":"Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001087583700008"],"pmid":["37704612"]},"author":[{"first_name":"Ewa","last_name":"Sitarska","full_name":"Sitarska, Ewa"},{"full_name":"Almeida, Silvia Dias","last_name":"Almeida","first_name":"Silvia Dias"},{"first_name":"Marianne Sandvold","last_name":"Beckwith","full_name":"Beckwith, Marianne Sandvold"},{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"full_name":"Czuchnowski, Jakub","last_name":"Czuchnowski","first_name":"Jakub"},{"last_name":"Siggel","full_name":"Siggel, Marc","first_name":"Marc"},{"full_name":"Roessner, Rita","last_name":"Roessner","first_name":"Rita"},{"first_name":"Aline","full_name":"Tschanz, Aline","last_name":"Tschanz"},{"first_name":"Christer","full_name":"Ejsing, Christer","last_name":"Ejsing"},{"full_name":"Schwab, Yannick","last_name":"Schwab","first_name":"Yannick"},{"full_name":"Kosinski, Jan","last_name":"Kosinski","first_name":"Jan"},{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"first_name":"Anna","last_name":"Erzberger","full_name":"Erzberger, Anna"},{"first_name":"Alba","full_name":"Diz-Muñoz, Alba","last_name":"Diz-Muñoz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Sitarska, Ewa, Silvia Dias Almeida, Marianne Sandvold Beckwith, Julian A Stopp, Jakub Czuchnowski, Marc Siggel, Rita Roessner, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-41173-1.","ista":"Sitarska E, Almeida SD, Beckwith MS, Stopp JA, Czuchnowski J, Siggel M, Roessner R, Tschanz A, Ejsing C, Schwab Y, Kosinski J, Sixt MK, Kreshuk A, Erzberger A, Diz-Muñoz A. 2023. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 14, 5644.","mla":"Sitarska, Ewa, et al. “Sensing Their Plasma Membrane Curvature Allows Migrating Cells to Circumvent Obstacles.” Nature Communications, vol. 14, 5644, Springer Nature, 2023, doi:10.1038/s41467-023-41173-1.","ama":"Sitarska E, Almeida SD, Beckwith MS, et al. Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. 2023;14. doi:10.1038/s41467-023-41173-1","apa":"Sitarska, E., Almeida, S. D., Beckwith, M. S., Stopp, J. A., Czuchnowski, J., Siggel, M., … Diz-Muñoz, A. (2023). Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-41173-1","short":"E. Sitarska, S.D. Almeida, M.S. Beckwith, J.A. Stopp, J. Czuchnowski, M. Siggel, R. Roessner, A. Tschanz, C. Ejsing, Y. Schwab, J. Kosinski, M.K. Sixt, A. Kreshuk, A. Erzberger, A. Diz-Muñoz, Nature Communications 14 (2023).","ieee":"E. Sitarska et al., “Sensing their plasma membrane curvature allows migrating cells to circumvent obstacles,” Nature Communications, vol. 14. Springer Nature, 2023."},"article_number":"5644","date_created":"2023-09-24T22:01:10Z","date_published":"2023-09-13T00:00:00Z","doi":"10.1038/s41467-023-41173-1","publication":"Nature Communications","day":"13","year":"2023","isi":1,"has_accepted_license":"1","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"We thank Jan Ellenberg, Leanne Strauss, Anusha Gopalan, and Jia Hui Li for critical feedback on the manuscript and the Life Science Editors for editing assistance. The plasmid with hSnx33 was a kind gift from Duanqing Pei. Cell line with GFP-tagged IRSp53 was a kind gift from Orion Weiner. We thank Brian Graziano for providing protocols, reagents, and key advice to generate CRISPR knockout HL-60 cells. We thank the EMBL flow cytometry core facility, the EMBL advanced light microscopy facility, the EMBL proteomics facility, and the EMBL genomics core facility for support and advice. We thank Anusha Gopalan and Martin Bergert for their support during mechanical measurements by AFM. We thank Estela Sosa Osorio for technical assistance for the co-immunoprecipitation. We thank the EMBL genome biology computational support (and specially Charles Girardot and Jelle Scholtalbers) for critical assistance during RNAseq analysis. We thank Hans Kristian Hannibal‐Bach for his technical assistance during the lipidomic analysis of plasma membrane isolates. We thank Steffen Burgold for their support with LLS7 microscope in the ZEISS Microscopy Customer Center Europe. We acknowledge the financial support of the European Molecular Biology Laboratory (EMBL) to A.D.-M., Y.S., A.K., and A.E., the EMBL Interdisciplinary Postdocs (EIPOD) program under Marie Sklodowska-Curie COFUND actions MSCA-COFUND-FP to M.S.B. and M. S. (grant agreement number: 847543), the BEST program funding by FCT (SFRH/BEST/150300/2019) to S.D.A. and the Joachim Herz Stiftung Add-on Fellowship for Interdisciplinary Science to E.S.\r\nOpen Access funding enabled and organized by Projekt DEAL."},{"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Immune responses rely on the rapid and coordinated migration of leukocytes. Whereas it is well established that single-cell migration is often guided by gradients of chemokines and other chemoattractants, it remains poorly understood how these gradients are generated, maintained, and modulated. By combining experimental data with theory on leukocyte chemotaxis guided by the G protein–coupled receptor (GPCR) CCR7, we demonstrate that in addition to its role as the sensory receptor that steers migration, CCR7 also acts as a generator and a modulator of chemotactic gradients. Upon exposure to the CCR7 ligand CCL19, dendritic cells (DCs) effectively internalize the receptor and ligand as part of the canonical GPCR desensitization response. We show that CCR7 internalization also acts as an effective sink for the chemoattractant, dynamically shaping the spatiotemporal distribution of the chemokine. This mechanism drives complex collective migration patterns, enabling DCs to create or sharpen chemotactic gradients. We further show that these self-generated gradients can sustain the long-range guidance of DCs, adapt collective migration patterns to the size and geometry of the environment, and provide a guidance cue for other comigrating cells. Such a dual role of CCR7 as a GPCR that both senses and consumes its ligand can thus provide a novel mode of cellular self-organization."}],"month":"09","intvolume":" 8","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1126/sciimmunol.adc9584","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2470-9468"]},"publication_status":"published","volume":8,"related_material":{"record":[{"relation":"research_data","id":"14279","status":"public"},{"relation":"dissertation_contains","id":"14697","status":"public"}]},"issue":"87","ec_funded":1,"_id":"14274","status":"public","keyword":["General Medicine","Immunology"],"type":"journal_article","article_type":"original","date_updated":"2023-12-21T14:30:01Z","department":[{"_id":"MiSi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"acknowledgement":"We thank I. de Vries and the Scientific Service Units (Life Sciences, Bioimaging, Nanofabrication, Preclinical and Miba Machine Shop) of the Institute of Science and Technology Austria for excellent support, as well as all the rotation students assisting in the laboratory work (B. Zens, H. Schön, and D. Babic).\r\nThis work was supported by grants from the European Research Council under the European Union’s Horizon 2020 research to M.S. (grant agreement no. 724373) and to E.H. (grant agreement no. 851288), and a grant by the Austrian Science Fund (DK Nanocell W1250-B20) to M.S. J.A. was supported by the Jenny and Antti Wihuri Foundation and Research Council of Finland's Flagship Programme InFLAMES (decision number: 357910). M.C.U. was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411.","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"day":"01","publication":"Science Immunology","isi":1,"year":"2023","doi":"10.1126/sciimmunol.adc9584","date_published":"2023-09-01T00:00:00Z","date_created":"2023-09-06T08:07:51Z","article_number":"adc9584","project":[{"grant_number":"724373","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Alanko, Jonna H, Mehmet C Ucar, Nikola Canigova, Julian A Stopp, Jan Schwarz, Jack Merrin, Edouard B Hannezo, and Michael K Sixt. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciimmunol.adc9584.","ista":"Alanko JH, Ucar MC, Canigova N, Stopp JA, Schwarz J, Merrin J, Hannezo EB, Sixt MK. 2023. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 8(87), adc9584.","mla":"Alanko, Jonna H., et al. “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Science Immunology, vol. 8, no. 87, adc9584, American Association for the Advancement of Science, 2023, doi:10.1126/sciimmunol.adc9584.","ieee":"J. H. Alanko et al., “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration,” Science Immunology, vol. 8, no. 87. American Association for the Advancement of Science, 2023.","short":"J.H. Alanko, M.C. Ucar, N. Canigova, J.A. Stopp, J. Schwarz, J. Merrin, E.B. Hannezo, M.K. Sixt, Science Immunology 8 (2023).","apa":"Alanko, J. H., Ucar, M. C., Canigova, N., Stopp, J. A., Schwarz, J., Merrin, J., … Sixt, M. K. (2023). CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. American Association for the Advancement of Science. https://doi.org/10.1126/sciimmunol.adc9584","ama":"Alanko JH, Ucar MC, Canigova N, et al. CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration. Science Immunology. 2023;8(87). doi:10.1126/sciimmunol.adc9584"},"title":"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration","author":[{"first_name":"Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061","full_name":"Alanko, Jonna H","last_name":"Alanko"},{"orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"id":"3795523E-F248-11E8-B48F-1D18A9856A87","first_name":"Nikola","orcid":"0000-0002-8518-5926","full_name":"Canigova, Nikola","last_name":"Canigova"},{"full_name":"Stopp, Julian A","last_name":"Stopp","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"},{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","full_name":"Schwarz, Jan"},{"full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"external_id":{"isi":["001062110600003"],"pmid":["37656776"]},"article_processing_charge":"No"},{"month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6328"},{"status":"public","id":"7885","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12272"},{"relation":"part_of_dissertation","status":"public","id":"14274"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"ec_funded":1,"file":[{"file_size":51585778,"date_updated":"2023-12-20T09:35:34Z","creator":"jstopp","file_name":"Thesis.pdf","date_created":"2023-12-20T09:35:34Z","embargo_to":"open_access","content_type":"application/pdf","relation":"main_file","access_level":"closed","embargo":"2024-12-20","checksum":"457927165d5d556305d3086f6b83e5c7","file_id":"14699"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f","file_size":69625950,"date_updated":"2023-12-20T10:41:42Z","creator":"jstopp","file_name":"Thesis.docx","date_created":"2023-12-20T09:35:35Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-99078-038-1"],"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","status":"public","type":"dissertation","_id":"14697","file_date_updated":"2023-12-20T10:41:42Z","department":[{"_id":"GradSch"},{"_id":"MiSi"}],"ddc":["570"],"supervisor":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-12-21T14:30:02Z","publisher":"Institute of Science and Technology Austria","date_published":"2023-12-20T00:00:00Z","doi":"10.15479/at:ista:14697","date_created":"2023-12-18T19:14:28Z","page":"226","day":"20","has_accepted_license":"1","year":"2023","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","author":[{"last_name":"Stopp","full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14697.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:10.15479/at:ista:14697","apa":"Stopp, J. A. (2023). Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14697","ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","mla":"Stopp, Julian A. Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14697."}},{"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"14684","checksum":"520bdb61e95e66070e02824947d2c5fa","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"Phd_Thesis_LA.pdf","date_created":"2023-12-13T15:37:55Z","creator":"larathoo","file_size":34101468,"date_updated":"2023-12-13T15:37:55Z"},{"content_type":"application/zip","access_level":"closed","relation":"source_file","checksum":"d8e59afd0817c98fba2564a264508e5c","file_id":"14685","date_updated":"2023-12-14T08:58:18Z","file_size":31052872,"creator":"larathoo","date_created":"2023-12-13T15:42:23Z","file_name":"Phd_Thesis_LA.zip"},{"date_created":"2023-12-11T19:24:59Z","file_name":"Supplementary_Materials.zip","date_updated":"2023-12-14T08:58:18Z","file_size":10713896,"creator":"larathoo","checksum":"9a778c949932286f4519e1f1fca2820d","file_id":"14681","content_type":"application/zip","access_level":"closed","relation":"supplementary_material"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663 - 337X"]},"ec_funded":1,"related_material":{"record":[{"status":"public","id":"11411","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism."}],"acknowledged_ssus":[{"_id":"ScienComp"}],"month":"12","alternative_title":["ISTA Thesis"],"ddc":["570"],"date_updated":"2023-12-22T11:04:45Z","supervisor":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"file_date_updated":"2023-12-14T08:58:18Z","_id":"14651","status":"public","type":"dissertation","day":"12","year":"2023","has_accepted_license":"1","date_created":"2023-12-11T19:30:37Z","doi":"10.15479/at:ista:14651","date_published":"2023-12-12T00:00:00Z","page":"96","oa":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:14651.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","mla":"Arathoon, Louise S. Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:14651.","short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:10.15479/at:ista:14651","apa":"Arathoon, L. S. (2023). Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14651"},"title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","article_processing_charge":"No","author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","last_name":"Arathoon","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S"}],"project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}]},{"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"status":"public","keyword":["Optimal transport","Hamilton-Jacobi equation","convex optimization"],"type":"preprint","article_number":"2312.12213","_id":"14703","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"title":"Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation","author":[{"id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","first_name":"Sadashige","last_name":"Ishida","full_name":"Ishida, Sadashige"},{"full_name":"Lavenant, Hugo","last_name":"Lavenant","first_name":"Hugo"}],"external_id":{"arxiv":["2312.12213"]},"article_processing_charge":"No","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-12-27T13:44:33Z","citation":{"ieee":"S. Ishida and H. Lavenant, “Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation,” arXiv. .","short":"S. Ishida, H. Lavenant, ArXiv (n.d.).","ama":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. doi:10.48550/arXiv.2312.12213","apa":"Ishida, S., & Lavenant, H. (n.d.). Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv. https://doi.org/10.48550/arXiv.2312.12213","mla":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, 2312.12213, doi:10.48550/arXiv.2312.12213.","ista":"Ishida S, Lavenant H. Quantitative convergence of a discretization of dynamic optimal transport using the dual formulation. arXiv, 2312.12213.","chicago":"Ishida, Sadashige, and Hugo Lavenant. “Quantitative Convergence of a Discretization of Dynamic Optimal Transport Using the Dual Formulation.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2312.12213."},"month":"12","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2312.12213"}],"oa_version":"Preprint","acknowledgement":"The authors would like to thank Chris Wojtan for his continuous support and several interesting discussions. Part of this research was performed during two visits: one of SI to the BIDSA research center at Bocconi University, and one of HL to the Institute of Science and Technology Austria. Both host institutions are warmly acknowledged for the hospital-\r\nity. HL is partially supported by the MUR-Prin 2022-202244A7YL “Gradient Flows and Non-Smooth Geometric Structures with Applications to Optimization and Machine Learning”, funded by the European Union - Next Generation EU. SI is supported in part by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council.","abstract":[{"text":"We present a discretization of the dynamic optimal transport problem for which we can obtain the convergence rate for the value of the transport cost to its continuous value when the temporal and spatial stepsize vanish. This convergence result does not require any regularity assumption on the measures, though experiments suggest that the rate is not sharp. Via an analysis of the duality gap we also obtain the convergence rates for the gradient of the optimal potentials and the velocity field under mild regularity assumptions. To obtain such rates we discretize the dual formulation of the dynamic optimal transport problem and use the mature literature related to the error due to discretizing the Hamilton-Jacobi equation.","lang":"eng"}],"doi":"10.48550/arXiv.2312.12213","date_published":"2023-12-19T00:00:00Z","date_created":"2023-12-21T10:14:37Z","day":"19","language":[{"iso":"eng"}],"publication":"arXiv","year":"2023","publication_status":"submitted"},{"date_created":"2023-12-31T23:01:02Z","doi":"10.1186/s12866-023-03147-7","date_published":"2023-12-01T00:00:00Z","year":"2023","has_accepted_license":"1","publication":"BMC Microbiology","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Open Access funding enabled and organized by Projekt DEAL. A.Y. and O.V.K. acknowledge financial support from the Klaus Faber Foundation. A.A.A. was funded by the Helmholtz AI project AMR-XAI. The work of O.O.B. is funded by Fonds zur Förderung der Wissenschaftlichen Forschung (FWF), Grant ESP 253-B.","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["38124060"]},"author":[{"full_name":"Yurtseven, Alper","last_name":"Yurtseven","first_name":"Alper"},{"id":"2F54A7BC-3902-11EA-AC87-BC9F3DDC885E","first_name":"Sofia","last_name":"Buyanova","full_name":"Buyanova, Sofia"},{"first_name":"Amay Ajaykumar A.","last_name":"Agrawal","full_name":"Agrawal, Amay Ajaykumar A."},{"last_name":"Bochkareva","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","first_name":"Olga"},{"last_name":"Kalinina","full_name":"Kalinina, Olga V V.","first_name":"Olga V V."}],"title":"Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis","citation":{"ista":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. 2023. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 23(1), 404.","chicago":"Yurtseven, Alper, Sofia Buyanova, Amay Ajaykumar A. Agrawal, Olga Bochkareva, and Olga V V. Kalinina. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology. Springer Nature, 2023. https://doi.org/10.1186/s12866-023-03147-7.","apa":"Yurtseven, A., Buyanova, S., Agrawal, A. A. A., Bochkareva, O., & Kalinina, O. V. V. (2023). Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. Springer Nature. https://doi.org/10.1186/s12866-023-03147-7","ama":"Yurtseven A, Buyanova S, Agrawal AAA, Bochkareva O, Kalinina OVV. Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis. BMC Microbiology. 2023;23(1). doi:10.1186/s12866-023-03147-7","short":"A. Yurtseven, S. Buyanova, A.A.A. Agrawal, O. Bochkareva, O.V.V. Kalinina, BMC Microbiology 23 (2023).","ieee":"A. Yurtseven, S. Buyanova, A. A. A. Agrawal, O. Bochkareva, and O. V. V. Kalinina, “Machine learning and phylogenetic analysis allow for predicting antibiotic resistance in M. tuberculosis,” BMC Microbiology, vol. 23, no. 1. Springer Nature, 2023.","mla":"Yurtseven, Alper, et al. “Machine Learning and Phylogenetic Analysis Allow for Predicting Antibiotic Resistance in M. Tuberculosis.” BMC Microbiology, vol. 23, no. 1, 404, Springer Nature, 2023, doi:10.1186/s12866-023-03147-7."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"404","issue":"1","volume":23,"publication_status":"published","publication_identifier":{"eissn":["1471-2180"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_BMCMicrobiology_Yurtseven.pdf","date_created":"2024-01-02T09:09:32Z","creator":"dernst","file_size":1979922,"date_updated":"2024-01-02T09:09:32Z","success":1,"checksum":"7ff5e95f3496ff663301eb4a13a316d5","file_id":"14723","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","intvolume":" 23","month":"12","abstract":[{"lang":"eng","text":"Background: Antimicrobial resistance (AMR) poses a significant global health threat, and an accurate prediction of bacterial resistance patterns is critical for effective treatment and control strategies. In recent years, machine learning (ML) approaches have emerged as powerful tools for analyzing large-scale bacterial AMR data. However, ML methods often ignore evolutionary relationships among bacterial strains, which can greatly impact performance of the ML methods, especially if resistance-associated features are attempted to be detected. Genome-wide association studies (GWAS) methods like linear mixed models accounts for the evolutionary relationships in bacteria, but they uncover only highly significant variants which have already been reported in literature.\r\n\r\nResults: In this work, we introduce a novel phylogeny-related parallelism score (PRPS), which measures whether a certain feature is correlated with the population structure of a set of samples. We demonstrate that PRPS can be used, in combination with SVM- and random forest-based models, to reduce the number of features in the analysis, while simultaneously increasing models’ performance. We applied our pipeline to publicly available AMR data from PATRIC database for Mycobacterium tuberculosis against six common antibiotics.\r\n\r\nConclusions: Using our pipeline, we re-discovered known resistance-associated mutations as well as new candidate mutations which can be related to resistance and not previously reported in the literature. We demonstrated that taking into account phylogenetic relationships not only improves the model performance, but also yields more biologically relevant predicted most contributing resistance markers."}],"pmid":1,"oa_version":"Published Version","department":[{"_id":"FyKo"}],"file_date_updated":"2024-01-02T09:09:32Z","date_updated":"2024-01-02T09:20:57Z","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public","_id":"14716"},{"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"14721","checksum":"818d6e13dd508f3a04f0941081022e5d","success":1,"date_updated":"2024-01-02T08:14:23Z","file_size":524321,"creator":"dernst","date_created":"2024-01-02T08:14:23Z","file_name":"2023_FMCAD_Pastva.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["9783854480600"]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. "}],"month":"10","scopus_import":"1","ddc":["000"],"date_updated":"2024-01-02T08:16:28Z","file_date_updated":"2024-01-02T08:14:23Z","department":[{"_id":"ToHe"}],"_id":"14718","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"location":"Ames, IA, United States","end_date":"2023-10-27","start_date":"2023-10-25","name":"FMCAD: Conference on Formal Methods in Computer-aided design"},"type":"conference","publication":"Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design","day":"01","year":"2023","has_accepted_license":"1","date_created":"2023-12-31T23:01:03Z","date_published":"2023-10-01T00:00:00Z","doi":"10.34727/2023/isbn.978-3-85448-060-0_20","page":"122-131","acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093.","oa":1,"publisher":"TU Vienna Academic Press","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–31, doi:10.34727/2023/isbn.978-3-85448-060-0_20.","apa":"Pastva, S., & Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design (pp. 122–131). Ames, IA, United States: TU Vienna Academic Press. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20","ama":"Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. TU Vienna Academic Press; 2023:122-131. doi:10.34727/2023/isbn.978-3-85448-060-0_20","ieee":"S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, Ames, IA, United States, 2023, pp. 122–131.","short":"S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Vienna Academic Press, 2023, pp. 122–131.","chicago":"Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, 122–31. TU Vienna Academic Press, 2023. https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20.","ista":"Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Conference on Formal Methods in Computer-aided design, 122–131."},"title":"Binary decision diagrams on modern hardware","article_processing_charge":"No","author":[{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","first_name":"Samuel","last_name":"Pastva","orcid":"0000-0003-1993-0331","full_name":"Pastva, Samuel"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}]},{"date_created":"2023-12-31T23:01:03Z","doi":"10.1093/qmath/haad008","date_published":"2023-12-01T00:00:00Z","page":"1253-1294","publication":"Quarterly Journal of Mathematics","day":"01","year":"2023","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","acknowledgement":"This work was done when both authors were visiting Institute of Science and Technology (IST) Austria. T.H. was being supported by Engineering and Physical Sciences Research Council grant EP/P026710/1. Y.K. had a great time there and is grateful for the hospitality. The appendix to this paper is largely based on a mini course T.H. had given at IST in February 2020.","title":"Equidistribution of primitive lattices in ℝn","external_id":{"arxiv":["2012.04508"]},"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Horesh, Tal","last_name":"Horesh","first_name":"Tal","id":"C8B7BF48-8D81-11E9-BCA9-F536E6697425"},{"full_name":"Karasik, Yakov","last_name":"Karasik","first_name":"Yakov"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics, vol. 74, no. 4, Oxford University Press, 2023, pp. 1253–94, doi:10.1093/qmath/haad008.","apa":"Horesh, T., & Karasik, Y. (2023). Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. Oxford University Press. https://doi.org/10.1093/qmath/haad008","ama":"Horesh T, Karasik Y. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 2023;74(4):1253-1294. doi:10.1093/qmath/haad008","ieee":"T. Horesh and Y. Karasik, “Equidistribution of primitive lattices in ℝn,” Quarterly Journal of Mathematics, vol. 74, no. 4. Oxford University Press, pp. 1253–1294, 2023.","short":"T. Horesh, Y. Karasik, Quarterly Journal of Mathematics 74 (2023) 1253–1294.","chicago":"Horesh, Tal, and Yakov Karasik. “Equidistribution of Primitive Lattices in ℝn.” Quarterly Journal of Mathematics. Oxford University Press, 2023. https://doi.org/10.1093/qmath/haad008.","ista":"Horesh T, Karasik Y. 2023. Equidistribution of primitive lattices in ℝn. Quarterly Journal of Mathematics. 74(4), 1253–1294."},"project":[{"grant_number":"EP-P026710-2","name":"Between rational and integral points","_id":"26A8D266-B435-11E9-9278-68D0E5697425"}],"issue":"4","volume":74,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_QuarterlyJourMath_Horesh.pdf","date_created":"2024-01-02T07:37:09Z","creator":"dernst","file_size":724748,"date_updated":"2024-01-02T07:37:09Z","success":1,"file_id":"14720","checksum":"bf29baa9eae8500f3374dbcb80712687","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"issn":["0033-5606"],"eissn":["1464-3847"]},"intvolume":" 74","month":"12","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"We count primitive lattices of rank d inside Zn as their covolume tends to infinity, with respect to certain parameters of such lattices. These parameters include, for example, the subspace that a lattice spans, namely its projection to the Grassmannian; its homothety class and its equivalence class modulo rescaling and rotation, often referred to as a shape. We add to a prior work of Schmidt by allowing sets in the spaces of parameters that are general enough to conclude the joint equidistribution of these parameters. In addition to the primitive d-lattices Λ themselves, we also consider their orthogonal complements in Zn, A1, and show that the equidistribution occurs jointly for Λ and A1. Finally, our asymptotic formulas for the number of primitive lattices include an explicit bound on the error term.","lang":"eng"}],"file_date_updated":"2024-01-02T07:37:09Z","department":[{"_id":"TiBr"}],"ddc":["510"],"date_updated":"2024-01-02T07:39:55Z","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14717"},{"citation":{"ista":"Mollania H, Zhang C, Du R, Qi X, Li J, Horta S, Ibáñez M, Keller C, Chenevier P, Oloomi-Buygi M, Cabot A. 2023. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 15(50), 58462–58475.","chicago":"Mollania, Hamid, Chaoqi Zhang, Ruifeng Du, Xueqiang Qi, Junshan Li, Sharona Horta, Maria Ibáñez, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces. American Chemical Society, 2023. https://doi.org/10.1021/acsami.3c14072.","short":"H. Mollania, C. Zhang, R. Du, X. Qi, J. Li, S. Horta, M. Ibáñez, C. Keller, P. Chenevier, M. Oloomi-Buygi, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 58462–58475.","ieee":"H. Mollania et al., “Nanostructured Li₂S cathodes for silicon-sulfur batteries,” ACS Applied Materials and Interfaces, vol. 15, no. 50. American Chemical Society, pp. 58462–58475, 2023.","ama":"Mollania H, Zhang C, Du R, et al. Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. 2023;15(50):58462–58475. doi:10.1021/acsami.3c14072","apa":"Mollania, H., Zhang, C., Du, R., Qi, X., Li, J., Horta, S., … Cabot, A. (2023). Nanostructured Li₂S cathodes for silicon-sulfur batteries. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.3c14072","mla":"Mollania, Hamid, et al. “Nanostructured Li₂S Cathodes for Silicon-Sulfur Batteries.” ACS Applied Materials and Interfaces, vol. 15, no. 50, American Chemical Society, 2023, pp. 58462–58475, doi:10.1021/acsami.3c14072."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"first_name":"Hamid","last_name":"Mollania","full_name":"Mollania, Hamid"},{"full_name":"Zhang, Chaoqi","last_name":"Zhang","first_name":"Chaoqi"},{"first_name":"Ruifeng","last_name":"Du","full_name":"Du, Ruifeng"},{"first_name":"Xueqiang","full_name":"Qi, Xueqiang","last_name":"Qi"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","first_name":"Sharona"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Caroline","full_name":"Keller, Caroline","last_name":"Keller"},{"last_name":"Chenevier","full_name":"Chenevier, Pascale","first_name":"Pascale"},{"full_name":"Oloomi-Buygi, Majid","last_name":"Oloomi-Buygi","first_name":"Majid"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"title":"Nanostructured Li₂S cathodes for silicon-sulfur batteries","acknowledgement":"The authors acknowledge the support from the 2BoSS project of the ERA-MIN3 program with the Spanish grant number PCI2022-132985/AEI/10.13039/501100011033 and the French grant number ANR-22-MIN3-0003-01. J.L. acknowledges the support from the Natural Science Foundation of Sichuan Province 2022NSFSC1229. The authors acknowledge the funding from Generalitat de Catalunya 2021 SGR 01581 and European Union NextGenerationEU/PRTR. This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NNF).","publisher":"American Chemical Society","quality_controlled":"1","year":"2023","publication":"ACS Applied Materials and Interfaces","day":"05","page":"58462–58475","date_created":"2023-12-31T23:01:03Z","date_published":"2023-12-05T00:00:00Z","doi":"10.1021/acsami.3c14072","_id":"14719","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-01-02T08:35:06Z","department":[{"_id":"MaIb"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"abstract":[{"text":"Lithium–sulfur batteries are regarded as an advantageous option for meeting the growing demand for high-energy-density storage, but their commercialization relies on solving the current limitations of both sulfur cathodes and lithium metal anodes. In this scenario, the implementation of lithium sulfide (Li2S) cathodes compatible with alternative anode materials such as silicon has the potential to alleviate the safety concerns associated with lithium metal. In this direction, here, we report a sulfur cathode based on Li2S nanocrystals grown on a catalytic host consisting of CoFeP nanoparticles supported on tubular carbon nitride. Nanosized Li2S is incorporated into the host by a scalable liquid infiltration–evaporation method. Theoretical calculations and experimental results demonstrate that the CoFeP–CN composite can boost the polysulfide adsorption/conversion reaction kinetics and strongly reduce the initial overpotential activation barrier by stretching the Li–S bonds of Li2S. Besides, the ultrasmall size of the Li2S particles in the Li2S–CoFeP–CN composite cathode facilitates the initial activation. Overall, the Li2S–CoFeP–CN electrodes exhibit a low activation barrier of 2.56 V, a high initial capacity of 991 mA h gLi2S–1, and outstanding cyclability with a small fading rate of 0.029% per cycle over 800 cycles. Moreover, Si/Li2S full cells are assembled using the nanostructured Li2S–CoFeP–CN cathode and a prelithiated anode based on graphite-supported silicon nanowires. These Si/Li2S cells demonstrate high initial discharge capacities above 900 mA h gLi2S–1 and good cyclability with a capacity fading rate of 0.28% per cycle over 150 cycles.","lang":"eng"}],"oa_version":"None","scopus_import":"1","intvolume":" 15","month":"12","publication_status":"published","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"language":[{"iso":"eng"}],"issue":"50","volume":15},{"department":[{"_id":"RoSe"}],"file_date_updated":"2024-01-02T08:45:07Z","date_updated":"2024-01-02T08:51:28Z","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"14715","volume":64,"issue":"12","publication_status":"published","publication_identifier":{"issn":["0022-2488"],"eissn":["1089-7658"]},"language":[{"iso":"eng"}],"file":[{"checksum":"66572f718a36465576cf0d6b3f7e01fc","file_id":"14722","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-02T08:45:07Z","file_name":"2023_JourMathPhysics_Mitrouskas.pdf","creator":"dernst","date_updated":"2024-01-02T08:45:07Z","file_size":4346922}],"scopus_import":"1","intvolume":" 64","month":"12","abstract":[{"lang":"eng","text":"We consider N trapped bosons in the mean-field limit with coupling constant λN = 1/(N − 1). The ground state of such systems exhibits Bose–Einstein condensation. We prove that the probability of finding ℓ particles outside the condensate wave function decays exponentially in ℓ."}],"oa_version":"Published Version","external_id":{"arxiv":["2307.11062"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Mitrouskas","full_name":"Mitrouskas, David Johannes","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"title":"Exponential decay of the number of excitations in the weakly interacting Bose gas","citation":{"chicago":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics. AIP Publishing, 2023. https://doi.org/10.1063/5.0172199.","ista":"Mitrouskas DJ, Pickl P. 2023. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 64(12), 121901.","mla":"Mitrouskas, David Johannes, and Peter Pickl. “Exponential Decay of the Number of Excitations in the Weakly Interacting Bose Gas.” Journal of Mathematical Physics, vol. 64, no. 12, 121901, AIP Publishing, 2023, doi:10.1063/5.0172199.","apa":"Mitrouskas, D. J., & Pickl, P. (2023). Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0172199","ama":"Mitrouskas DJ, Pickl P. Exponential decay of the number of excitations in the weakly interacting Bose gas. Journal of Mathematical Physics. 2023;64(12). doi:10.1063/5.0172199","ieee":"D. J. Mitrouskas and P. Pickl, “Exponential decay of the number of excitations in the weakly interacting Bose gas,” Journal of Mathematical Physics, vol. 64, no. 12. AIP Publishing, 2023.","short":"D.J. Mitrouskas, P. Pickl, Journal of Mathematical Physics 64 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"121901","date_created":"2023-12-31T23:01:02Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1063/5.0172199","year":"2023","has_accepted_license":"1","publication":"Journal of Mathematical Physics","day":"01","oa":1,"quality_controlled":"1","publisher":"AIP Publishing","acknowledgement":"We thank Lea Boßmann, Phan Thành Nam and Simone Rademacher for helpful remarks. P.P. acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Grant No. SFB/TRR 352 “Mathematics of Many-Body Quantum Systems and Their Collective Phenomena.”"},{"citation":{"chicago":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592098.","ista":"Jeschke S, Wojtan C. 2023. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 42(4), 83.","mla":"Jeschke, Stefan, and Chris Wojtan. “Generalizing Shallow Water Simulations with Dispersive Surface Waves.” ACM Transactions on Graphics, vol. 42, no. 4, 83, Association for Computing Machinery, 2023, doi:10.1145/3592098.","ama":"Jeschke S, Wojtan C. Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. 2023;42(4). doi:10.1145/3592098","apa":"Jeschke, S., & Wojtan, C. (2023). Generalizing shallow water simulations with dispersive surface waves. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3592098","ieee":"S. Jeschke and C. Wojtan, “Generalizing shallow water simulations with dispersive surface waves,” ACM Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.","short":"S. Jeschke, C. Wojtan, ACM Transactions on Graphics 42 (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Jeschke, Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"external_id":{"isi":["001044671300049"]},"article_processing_charge":"Yes (in subscription journal)","title":"Generalizing shallow water simulations with dispersive surface waves","article_number":"83","project":[{"grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"ACM Transactions on Graphics","date_published":"2023-08-01T00:00:00Z","doi":"10.1145/3592098","date_created":"2023-08-27T22:01:17Z","acknowledgement":"We thank Georg Sperl for helping with early research for this paper, Mickael Ly and Yi-Lu Chen for proofreading, and members of the ISTA Visual Computing Group for general feedback. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).\r\nThe motorboat and sailboat were modeled by Sergei and the palmtrees by YadroGames. The environment map was created by Emil Persson.","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"date_updated":"2024-01-02T09:35:55Z","ddc":["000"],"department":[{"_id":"ChWo"}],"file_date_updated":"2024-01-02T09:34:27Z","_id":"14240","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"publication_status":"published","file":[{"content_type":"video/mp4","access_level":"open_access","relation":"main_file","file_id":"14704","checksum":"1d178bb2f8011d9f5aedda6427e18c7a","success":1,"date_updated":"2023-12-21T12:26:40Z","file_size":511572575,"creator":"sjeschke","date_created":"2023-12-21T12:26:40Z","file_name":"PaperVideo_final.mp4"},{"file_id":"14725","checksum":"a49b2e744d5cd1276bb8b2e0ce6dc638","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-01-02T09:34:27Z","file_name":"2023_ACMToG_Jeschke.pdf","date_updated":"2024-01-02T09:34:27Z","file_size":7469177,"creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"4","volume":42,"acknowledged_ssus":[{"_id":"ScienComp"}],"abstract":[{"lang":"eng","text":"This paper introduces a novel method for simulating large bodies of water as a height field. At the start of each time step, we partition the waves into a bulk flow (which approximately satisfies the assumptions of the shallow water equations) and surface waves (which approximately satisfy the assumptions of Airy wave theory). We then solve the two wave regimes separately using appropriate state-of-the-art techniques, and re-combine the resulting wave velocities at the end of each step. This strategy leads to the first heightfield wave model capable of simulating complex interactions between both deep and shallow water effects, like the waves from a boat wake sloshing up onto a beach, or a dam break producing wave interference patterns and eddies. We also analyze the numerical dispersion created by our method and derive an exact correction factor for waves at a constant water depth, giving us a numerically perfect re-creation of theoretical water wave dispersion patterns."}],"oa_version":"Published Version","scopus_import":"1","month":"08","intvolume":" 42"},{"acknowledgement":"We thank Lucy Colwell for suggesting that we use covariance based methods to predict contacts and Yang Hsia, Scott Boyken, Zibo Chen, and David Baker for collaborations on designed protein complexes. We also thank Ned Wingreen for suggesting the alternative derivation of (11). This research was supported by the Office of Naval Research through ONR N00014-17-1-3029, the Simons Foundation the NSF-Simons Center for Mathematical and Statistical Analysis of Biology at Harvard (award number #1764269), the Peter B. Lewis ’55 Lewis-Sigler Institute/Genomics Fund through the Lewis-Sigler Institute of Integrative Genomics at Princeton University, and the National Science Foundation through the Center for the Physics of Biological Function (PHY-1734030).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"day":"01","publication":"Nature Communications","has_accepted_license":"1","year":"2023","date_published":"2023-12-01T00:00:00Z","doi":"10.1038/s41467-023-43168-4","date_created":"2023-12-24T23:00:53Z","article_number":"8328","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Curatolo, Agnese I., Ofer Kimchi, Carl Peter Goodrich, Ryan K. Krueger, and Michael P. Brenner. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-43168-4.","ista":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. 2023. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 14, 8328.","mla":"Curatolo, Agnese I., et al. “A Computational Toolbox for the Assembly Yield of Complex and Heterogeneous Structures.” Nature Communications, vol. 14, 8328, Springer Nature, 2023, doi:10.1038/s41467-023-43168-4.","apa":"Curatolo, A. I., Kimchi, O., Goodrich, C. P., Krueger, R. K., & Brenner, M. P. (2023). A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-43168-4","ama":"Curatolo AI, Kimchi O, Goodrich CP, Krueger RK, Brenner MP. A computational toolbox for the assembly yield of complex and heterogeneous structures. Nature Communications. 2023;14. doi:10.1038/s41467-023-43168-4","ieee":"A. I. Curatolo, O. Kimchi, C. P. Goodrich, R. K. Krueger, and M. P. Brenner, “A computational toolbox for the assembly yield of complex and heterogeneous structures,” Nature Communications, vol. 14. Springer Nature, 2023.","short":"A.I. Curatolo, O. Kimchi, C.P. Goodrich, R.K. Krueger, M.P. Brenner, Nature Communications 14 (2023)."},"title":"A computational toolbox for the assembly yield of complex and heterogeneous structures","author":[{"full_name":"Curatolo, Agnese I.","last_name":"Curatolo","first_name":"Agnese I."},{"first_name":"Ofer","last_name":"Kimchi","full_name":"Kimchi, Ofer"},{"first_name":"Carl Peter","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","orcid":"0000-0002-1307-5074","full_name":"Goodrich, Carl Peter"},{"first_name":"Ryan K.","full_name":"Krueger, Ryan K.","last_name":"Krueger"},{"first_name":"Michael P.","full_name":"Brenner, Michael P.","last_name":"Brenner"}],"article_processing_charge":"Yes","oa_version":"Published Version","abstract":[{"text":"The self-assembly of complex structures from a set of non-identical building blocks is a hallmark of soft matter and biological systems, including protein complexes, colloidal clusters, and DNA-based assemblies. Predicting the dependence of the equilibrium assembly yield on the concentrations and interaction energies of building blocks is highly challenging, owing to the difficulty of computing the entropic contributions to the free energy of the many structures that compete with the ground state configuration. While these calculations yield well known results for spherically symmetric building blocks, they do not hold when the building blocks have internal rotational degrees of freedom. Here we present an approach for solving this problem that works with arbitrary building blocks, including proteins with known structure and complex colloidal building blocks. Our algorithm combines classical statistical mechanics with recently developed computational tools for automatic differentiation. Automatic differentiation allows efficient evaluation of equilibrium averages over configurations that would otherwise be intractable. We demonstrate the validity of our framework by comparison to molecular dynamics simulations of simple examples, and apply it to calculate the yield curves for known protein complexes and for the assembly of colloidal shells.","lang":"eng"}],"month":"12","intvolume":" 14","scopus_import":"1","file":[{"success":1,"file_id":"14714","checksum":"fd9e9d527c2691f03fbc24031a75a3b3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_NatureComm_Curatolo.pdf","date_created":"2023-12-27T08:40:43Z","creator":"kschuh","file_size":1342319,"date_updated":"2023-12-27T08:40:43Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20411723"]},"publication_status":"published","volume":14,"_id":"14710","status":"public","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["530"],"date_updated":"2024-01-02T11:36:46Z","file_date_updated":"2023-12-27T08:40:43Z","department":[{"_id":"CaGo"}]},{"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Amid the delays due to the global pandemic, in early October 2022, the auxin community gathered in the idyllic peninsula of Cavtat, Croatia. More than 170 scientists from across the world converged to discuss the latest advancements in fundamental and applied research in the field. The topics, from signalling and transport to plant architecture and response to the environment, show how auxin research must bridge from the molecular realm to macroscopic developmental responses. This is mirrored in this collection of reviews, contributed by participants of the Auxin 2022 meeting.","lang":"eng"}],"intvolume":" 74","month":"12","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2024-01-02T09:23:57Z","file_size":425194,"date_created":"2024-01-02T09:23:57Z","file_name":"2023_JourExperimentalBotany_DelBianco.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f66fb960fd791dea53fd0e087f2fbbe8","file_id":"14724","success":1}],"publication_status":"published","publication_identifier":{"eissn":["1460-2431"],"issn":["0022-0957"]},"volume":74,"issue":"22","_id":"14709","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","ddc":["580"],"date_updated":"2024-01-02T09:29:24Z","department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-02T09:23:57Z","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","publication":"Journal of Experimental Botany","day":"01","year":"2023","has_accepted_license":"1","date_created":"2023-12-24T23:00:53Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1093/jxb/erad420","page":"6889-6892","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Del Bianco, J. Friml, L. Strader, S. Kepinski, Journal of Experimental Botany 74 (2023) 6889–6892.","ieee":"M. Del Bianco, J. Friml, L. Strader, and S. Kepinski, “Auxin research: Creating tools for a greener future,” Journal of Experimental Botany, vol. 74, no. 22. Oxford University Press, pp. 6889–6892, 2023.","ama":"Del Bianco M, Friml J, Strader L, Kepinski S. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 2023;74(22):6889-6892. doi:10.1093/jxb/erad420","apa":"Del Bianco, M., Friml, J., Strader, L., & Kepinski, S. (2023). Auxin research: Creating tools for a greener future. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/erad420","mla":"Del Bianco, Marta, et al. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany, vol. 74, no. 22, Oxford University Press, 2023, pp. 6889–92, doi:10.1093/jxb/erad420.","ista":"Del Bianco M, Friml J, Strader L, Kepinski S. 2023. Auxin research: Creating tools for a greener future. Journal of Experimental Botany. 74(22), 6889–6892.","chicago":"Del Bianco, Marta, Jiří Friml, Lucia Strader, and Stefan Kepinski. “Auxin Research: Creating Tools for a Greener Future.” Journal of Experimental Botany. Oxford University Press, 2023. https://doi.org/10.1093/jxb/erad420."},"title":"Auxin research: Creating tools for a greener future","external_id":{"pmid":["38038239"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"full_name":"Del Bianco, Marta","last_name":"Del Bianco","first_name":"Marta"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Strader, Lucia","last_name":"Strader","first_name":"Lucia"},{"first_name":"Stefan","full_name":"Kepinski, Stefan","last_name":"Kepinski"}]}]